Wilson took charge at Victoria Park in the summer of 2006, having had spells in charge of Barnsley, Sheffield Wednesday, Bristol City and MK Dons.
A short statement on the club's official website read: "Danny Wilson has left the services of Hartlepool United Football Club.
"Chris Turner will be in temporary charge of first-team affairs as well as carrying out his duties as director of sport.
"The club would like to thank Danny for the hard work he has put in during his time at Victoria Park and wish him all the best for the future."
Pools are 13th in the table and have not won any of their last six league games, having drawn 1-1 at Hereford United at the weekend.