Passing the motion was a response to her failure to stop the persecution of the Rohingya minority in her country.
Ms Suu Kyi won the Nobel Peace Prize in 1991 for her efforts to bring democracy to Myanmar - also known as Burma - which was then under military rule.
A UN report last month said Myanmar military leaders must be investigated for genocide against the Rohingyas.
At least 700,000 Rohingya fled violence in the country in the past 12 months.
The move by MPs in the House of Commons came a day after Prime Minister Justin Trudeau said that parliament was reconsidering whether Ms Suu Kyi still deserved the honour of citizenship.
But Mr Trudeau also said the move would not end the plight of hundreds of thousands of Rohingya people, a Muslim minority which is stateless in majority-Buddhist Myanmar.
In 2007 Canada granted honorary citizenship to Ms Suu Kyi, just one of six people to be so recognised.