Thomson will join former Highlanders' team-mates Callum Bruce and Kane Thompson as well as former All Black Isaia Toeava at the club.
"I'm excited to be embarking on the next stage of my career with the Canon Eagles in 2013 but jointly saddened to be closing a significant chapter of my life. I'm humbled and proud to have had the opportunity to represent Otago, the Highlanders and the All Blacks throughout my career," Thomson said in a statement.
"The experiences and friendships I have made will last a lifetime and my heart will always remain with New Zealand rugby. I will be forever grateful to the coaches, fellow players, and fans that have made this journey possible."
Thomson played 29 tests and scored six tries for the All Blacks since making his test debut against Ireland in 2008 and was part of the Rugby World Cup-winning side in 2011.
He has represented New Zealand almost continuously, in various teams, for more than a decade, having also played for New Zealand Schools, New Zealand under-19s, New Zealand under-21s and the New Zealand sevens team.
All Blacks coach Steve Hansen said: "On behalf of the All Blacks, we want to wish Adam well on the next step of his rugby career. He is an outstanding, world-class loose forward who always gave his very best."
