The invention discloses a method for treating trapped gas in a deepwater blowout preventer stack. The method includes the following steps that S1, the underwater blowout preventer stack is switched off, and positive cycle well killing is conducted; S2, after well killing, heavy sizing enters a marine riser boosting pipeline through replacement, and the marine riser boosting pipeline is opened; S3, the underwater blowout preventer stack is switched on, a well killing pipeline and a flow resisting pipeline are closed, slurry is poured to a marine riser until the liquid level of an annulus is not reduced, and then the underwater blowout preventer stack is switched off; S4, the slurry circulates in the well killing pipeline and the flow resisting pipeline, and the trapped gas circulates out; S5, the trapped gas circulates until no gas is returned basically, the underwater blowout preventer stack is switched on, and a pull is made. Due to the fact that the specific gravity of the heavy sizing is large, the trapped gas in the underwater blowout preventer stack is pressed downwards through the heavy sizing, the trapped gas enters the well killing pipeline and the flow resisting pipeline of the underwater blowout preventer stack, and when the slurry circulates in the well killing pipeline and the flow resisting pipeline, the trapped gas can circulate out from the flow resisting pipeline. A novel trapped gas treatment thought is provided for deepwater work, and the trapped gas treatment risk in deepwater work can be reduced.