During the 2007 season, Jones stayed near the top of the rankings in three-point shooting percentage, finishing third in the league, with a shooting percentage of 44.4%. Despite his good shooting for the year, Jones was not selected to participate in the Three-point Shootout contest during the 2008 NBA All-Star Game, much to the chagrin of Trail Blazers fans.
On June 26, 2008, Jones used his player option to opt out of his contract with the Trail Blazers, making him a free agent for the off-season.
On July 9, 2008, Jones signed a contract with his hometown team, the Miami Heat. He earned $4 million in his first year of a potential five-year contract, worth up to $23.2 million. The first two years were guaranteed, while the final three were options held by both the Miami Heat and Jones.
On June 29, 2010, he was released to clear salary cap space worth $400,000. On July 19, 2010, Jones was re-signed by the Miami Heat for the league minimum.
On December 9, 2011, Jones re-signed with the Heat to a three-year, $4.5 million contract.
In the 2012–13 season, an impressive playoff run by the Heat culminated in Jones' first NBA championship, and the franchise's second as they defeated the Oklahoma City Thunder in the 2012 NBA Finals, 4 games to 1. He won his second championship the following season, when the Heat defeated the San Antonio Spurs in seven games. In 2013–14, the Heat made the 2014 NBA Finals as they recorded their fourth straight Finals appearance. Miami faced the Spurs again but this time, the Heat went on to lose in five games.