A method for controlling a base sequence determination, wherein the base sequence determination comprises a first biochemical reaction, a second biochemical reaction, and photographing, wherein the first biochemical reaction and the second biochemical reaction are carried out on a reaction device, and a sequence determination system is used to control the base sequence determination, wherein the sequence determination system includes a fluid device and an optical device, the reaction device is connected to the fluid device; the reaction device includes a first component and a second component, each of the first component and the second component is provided with a sample; the optical device comprises a second control unit, a drive platform, an image acquisition unit and a light source, the second control unit including an upper computer to transmit an initialization command and a lower computer to transmit a drive command according to the initialization command; and, a repeated executable unit included in the base sequence determination is defined as: a second biochemical reaction - a first biochemical reaction - photographing; wherein the method includes performing as initial steps: a. performing the first biochemical reaction on the sample of the first component by using the fluid device, b. photographing the sample of the first component after the first biochemical reaction by using the optical device, and c. performing the first biochemical reaction on the sample of the second component by using the fluid device; and wherein the method includes, after completion of the initial steps, performing the repeated executable unit at least once on each of the samples of the first and second component in such a manner that while the second biochemical reaction and/or the first biochemical reaction of the repeated executable unit is performed on the sample of one of the first component and the second component by using the fluid device, photographing of the repeated executable unit of the sample of the other component is performed with the optical device; the method further comprising: determining a plurality of set positions for the optical device by the drive platform according to the initialization command; moving the reaction device by the drive platform according to the plurality of set positions and the drive command when using the optical device to photograph the sample on the first component and/or the second component; when the drive platform moves the reaction device to the set position, controlling the light source by the lower computer to emit light to excite the sample to emit light for detection; controlling the image acquisition unit by the lower computer to acquire the detection light to form the image data; and transferring the image data from the acquisition unit directly to the upper computer. a. performing the first biochemical reaction on the sample of the first component by using the fluid device, b. photographing the sample of the first component after the first biochemical reaction by using the optical device, and c. performing the first biochemical reaction on the sample of the second component by using the fluid device; determining a plurality of set positions for the optical device by the drive platform according to the initialization command; moving the reaction device by the drive platform according to the plurality of set positions and the drive command when using the optical device to photograph the sample on the first component and/or the second component; when the drive platform moves the reaction device to the set position, controlling the light source by the lower computer to emit light to excite the sample to emit light for detection; controlling the image acquisition unit by the lower computer to acquire the detection light to form the image data; and transferring the image data from the acquisition unit directly to the upper computer.