Thompson, 21, played three games this season for a career total of 14.
The athletic backman stepped up in the absence of injured pair Daniel Talia and Sam Shaw late in the year, holding down a key post in defence in finals against Fremantle and Hawthorn.
Crows football operations general manager Phil Harper said: “We are very pleased that Luke has decided he wants to continue his career with us. He played some great SANFL football this year but had to be patient waiting for AFL opportunities.
“His form in the last two finals was very good, which was no surprise as we know Luke’s capabilities. He had a frustrating year trying to break into the senior side and we are really pleased that despite this he has decided to stay with the Club, as he sees a bright future for this team.
“Luke is the last of the primary listed players to be recontracted with the remainder of the 2012 rookie list players to be contracted in the next few weeks.”
Originally from Timboon near Geelong, Thompson joined Adelaide as a rookie with pick No.17 in December, 2009. He was elevated to the senior list at the end of 2010 and made his AFL debut against Port Adelaide in Round Four, 2011.
He was a member of Woodville-West Torrens premiership team last year.