The 36-year-old has committed to the Paisley club despite their relegation from the Premiership as the division’s bottom side.
Thompson scored four times for the team he grew up supporting last term as he suffered an injury-interrupted campaign because of a groin problem.
He also made headlines in April for his part in a bizarre training-ground incident involving team-mate John McGinn.
The striker injured his colleague when he threw a spiked pole in his direction and speared the Scotland U21 midfielder in the thigh. McGinn has since begun legal proceedings against the club.
Thompson has been at St Mirren since leaving Burnley in 2011 and has scored 52 goals in 146 appearances.
The former Scotland international started his career with Dundee United and has also spent spells with Rangers and Cardiff City.
Thompson told the official club website: “After the disappointments of last year I am super motivated to make sure I enjoy this season and help St Mirren challenge in the Championship.
“Last season was hugely disappointing missing half the season through injury but with a good pre-season behind me and having worked really hard over the close season I am confident I can be an asset to the team.”
Thompson’s extended stay is a further boost for new St Mirren manager Ian Murray, who has also added Scott Agnew to his squad.
The former Rangers midfielder arrives from Murray’s old club Dumbarton after four years there and he has also agreed a one-year deal.
Murray said: “Scott has the quality to step up to full-time football and do well at St Mirren. I am delighted to have Thommo on board for the season ahead.
“I know him very well having played together in the past and know he will be a big goal threat for us in the new season. His experience will be invaluable for the younger players.”