The invention discloses a method for controlling a sequence determination reaction. A sequence determination system is used for controlling the sequence determination reaction. The sequence determination system comprises a fluid device. In the fluid device, a valve body assembly comprises a first valve and a second valve; the first valve comprises a stator and a rotor, and has a common port; the stator has a plurality of ports; and a communication groove is arranged on the rotor. The method comprises the following steps: allowing a first port to communicate with the common port through the communication groove; allowing the second valve to communicate with a first reagent and the first port; allowing the first reagent to successively pass through the second valve and the first valve and then enter a reaction unit in virtue of a driving component so as to realize a first biochemical reaction; allowing the second valve to communicate with a first buffer and the first port before rotatingof the rotor; and allowing the first buffer to successively pass through the second valve and the first valve in virtue of the driving component. According to the method, before the rotor is rotated,the first valve is washed with the first buffer; that is, the first reagent in the first valve is replaced, so the risk of cross-contamination when the rotor switches different reagents can be avoided.