A replacement has not been named but the Warriors have an attractive roster and the position will be an attractive one among the top coaching candidates seeking employment.
"Mark has accomplished many good things during his three years with the organization, including his role in helping elevate this team into a better position than it was when he arrived nearly 36 months ago," Warriors General Manager Bob Myers said in a statement.
"We're appreciative of his dedication and commitment since his arrival and are extremely grateful for his contributions. However, as an organization, we simply feel it's best to move in a different direction at this time."
Jackson, 49, took over a Warriors team that went 36-46 in the 2010-11 campaign and, three seasons later, became the third head coach in franchise history to lead the team to at least 50 wins in a campaign.
The Warriors went 51-31 during the regular season, which left them sixth in the 15-team Western Conference, and went on to lose a decisive seventh game to the Los Angeles Clippers in the first round of the playoffs.
Jackson, who had a year left on his contract, went 121-109 in his three seasons, including two trips to the playoffs.