The 36-year-old started his career with the Shrimps and helped them win promotion to the Football League, scoring in their play-off final win over Exeter in 2007.
"I'm absolutely buzzing to be honest. I'm so glad to be back," Thompson said.
Morecambe have also re-signed 34-year-old midfielder Michael Rose on a one-year deal.
Rose made 50 appearances for the Shrimps last season after joining on a one-year deal in August.
"I spoke to the manager last season and there was never really any doubts in my mind that I would re-sign," he said.
Find all the latest football transfers on our dedicated page.
Morecambe have re-signed veteran forward Garry Thompson on a one-year deal after his release by Wycombe.