The move, which could lead to tariffs on a key Canadian export, came a week after Canada said it would impose new border taxes on Chinese-made electric vehicles, steel and aluminium.
Beijing also said it would file a complaint with the World Trade Organization over the EV tariffs, which it criticised as "discriminatory" and "unilateral".
Canada's minister of agriculture said plans for the canola investigation were "deeply concerning" and the government was closely monitoring the situation.
The latest tit-for-tat comes as a rising number of governments, including the US and European Union, erect barriers against Chinese-made electric cars.
In announcing the EV tariffs last week, Canadian Prime Minister Justin Trudeau said countries such as China had "chosen to give themselves an unfair advantage in the global marketplace".
Western countries allege that Chinese firms are benefiting from subsidies and other government help, allowing for "dumping", which is when product is sold below cost, making it difficult for other firms to compete.