After a nearly three-year hiatus, during which several band members worked on independent projects, Bon Jovi regrouped in 1999 to begin work on their next studio album. Their 2000 release, Crush, enjoyed overwhelming success both in the US and overseas, thanks in part to the smash-hit single "It's My Life", co-written by famous Swedish producer Max Martin. Crush, which also produced such hits as "Say It Isn't So" and "Thank You for Loving Me", soon became the band's most successful studio album since Keep the Faith, and helped introduce Bon Jovi to a new, younger fan base. The Crush Tour, which began that summer, originally encompassed only 60 or so shows and was extended due to Bon Jovi's newfound popularity, with the band remaining on tour through mid-2001. While on tour, Bon Jovi released a collection of live performances from throughout their career in an album entitled, One Wild Night: Live 1985-2001. The crush tour was notable in that the European 2000 leg included the band headlining two nights at Wembley Stadium, these would be the final shows ever at the venue before it was demolished.

Shortly after the terrorist attacks of September 11, 2001, the band performed as part of the historic star-studded The Concert for New York City benefit concert for victims and their families. They performed an acoustic medley of "Livin' on a Prayer" and "Wanted Dead or Alive" with a stirring finale of "It's My Life".

In late 2002, Bounce, the band's follow-up to Crush, hit stores. Though Bounce did not enjoy quite the level of success of its predecessor, the album did produce the hit singles, "Everyday" and "Misunderstood". The band went on a U.S. tour for this album, during which they made history as the last band to play Veterans Stadium in Philadelphia before it was torn down. The band also released a promotional album through Target. The album featured eight demo and live tracks.

Following the Bounce Tour, which wrapped up in August 2003, Bon Jovi embarked on what would become a unique and ambitious project. Originally intending to produce an album consisting of live acoustic performances of various songs, the band ended up rewriting, re-recording and reinventing 12 of their biggest hits in a new and much different light. This Left Feels Right was released in November 2003, with the title referring to the "left turn" of sorts that the band took in redoing the songs heard on this record.

The following year the band released a box set entitled 100,000,000 Bon Jovi Fans Can't Be Wrong, the title an homage to Elvis Presley's 50,000,000 Elvis Fans Can't Be Wrong. The set consisted of four CDs packed with 38 unreleased and 12 rare tracks, as well as a DVD. The box set marked the sales of 100 million Bon Jovi albums and also commemorated the 20th anniversary of the release of the band's first record in 1984. In November 2004, Bon Jovi was honored with the award for Merit at the American Music Awards, where they performed a sneak preview of an unfinished song, "Have a Nice Day".

Bon Jovi participated in Live 8 on July 2, 2005. The full, final version of "Have a Nice Day" was debuted at the event, alongside the classics, "Livin' on a Prayer" and "It's My Life".

On August 20th, 2005, Bon Jovi headlined Miller Brewing Co.'s Big Brew-Ha, celebrating its 150th anniversary. The free stadium concert at Miller Park in Milwaukee included one preview song from the band's forthcoming album.

In September 2005, Bon Jovi was honored with the Diamond Award at the World Music Awards for selling 100 million albums. To date, they have sold 120 million albums (excluding singles) worldwide.

Bon Jovi's long-awaited new album, Have a Nice Day, was released on September 20th, 2005 (U.S.), followed by an international tour which kicked off in early November. The album topped the charts around the world, landing on the number two spot on the U.S Billboards during the first week of sales. Bon Jovi had a career-best first week, selling over 202,000 albums. "Have A Nice Day" was the first single off the new album, and debuted at radio worldwide on July 18, 2005. The second single, "Who Says You Can't Go Home", has since debuted as well, including a duet version with country singer Jennifer Nettles of the band Sugarland. In May of 2006, Bon Jovi made history by becoming the first Rock & Roll Band to have a #1 hit on Billboard's Hot Country Chart. The third single in the album is entitled "Welcome to Wherever You Are".

Soon after the release of Have A Nice Day, the band started gearing up for a new 2005/2006-world tour. This tour, being shorter than previous ones with only seventy-five shows planned - brings the band to numerous stages and arenas throughout the world. Originally it was planned for them to be the first act to perform at the new Wembley Stadium, however, the construction company Multiplex who are behind the stadium's rebuilding project have said that the stadium will not be ready until 2007. The concert was therefore moved to the Milton Keynes National Bowl with the same performance dates. 1 2 Following dates in Japan and Europe, Bon Jovi extended the tour and returned to the US in the summer of 2006 for a few stadium shows, including 3 shows in the band's native New Jersey at Giants Stadium as well as in Philadelphia, Boston, Pittsburgh, and Chicago.

On January 21, 2006, in Hamilton, Ontario, Bon Jovi's plane overshot and skidded off the runway after a show in Buffalo; the band members were unharmed.

On February 7, 2006, a promotional album, Live from the Have a Nice Day Tour, was released through Wal-Mart. It contains six live tracks recorded in December 2005 in Boston.

On February 19, 2006, Bon Jovi performed as the headlining act prior to Nascar's Daytona 500. The band performed "It's My Life" and their two new singles "Have a Nice Day" and "Who Says You Can't Go Home", the latter with Jennifer Nettles. The country version of this song would hit #1 on the Country Billboard Charts on May 6, 2006.

On May 13, 2006, Bon Jovi kicked off their European leg of the "Have A Nice Day" tour in Dusseldorf, Germany. During the encore, they played the 10 minute epic "Dry County", from 1992's Keep The Faith, for the first time in ten years, to the delight of their fans.

On July 29, 2006, the band played their final show of their Have A Nice Day Tour to a sold out crowd of 55,000 at Giants Stadium. Jon Bon Jovi thanked the crowd for their support because it was the 8th time the group had sold out Giants Stadium.

On September 7, 2006, Bon Jovi, along with other top recording artists, participated in Fashion Rocks. The red carpet event, held at Radio City Music Hall, kicked off New York's Fashion Week. The concert, curated by Elton John, raised money for the Elton John AIDS Foundation. Bon Jovi began with an acoustic rendition of "Livin' on a Prayer," then jumped into a spectacular full electric performance of their latest single "Who Says You Can't Go Home."

Also on September 20, 2006, a Hurricane Katrina-based episode of Oprah was broadcast. At the end of the program, Bon Jovi performed "Who Says You Can't Go Home" to suit the Hurricane Katrina theme.

On October 13, 2006, it was announced that Bon Jovi were to be inducted into the UK Music Hall of Fame, joining music legends such as The Beatles, The Rolling Stones, U2, Madonna and Elvis Presley. At the awards ceremony on November 14, 2006, Bon Jovi performed acoustic versions of "Livin' on a Prayer" and "Wanted Dead or Alive", along with "It's My Life".

On February 11, 2007, Bon Jovi finally won the elusive Grammy Award for "Best Country Collaboration with Vocals" for "Who Says You Can't Go Home".