The invention discloses a gene sequencing instrument, a control device and method of the gene sequencing instrument. The device includes a first controller used for transmitting an initialization instruction, a random access memory used for storing sequencing flow control information, and a second controller which is connected with the first controller and the random access memory and is used for receiving the initialization instruction, performing initialization configuration on devices in the gene sequencing instrument according to the initialization instruction, reading the sequencing flow control information from the random access memory, and controlling the devices in the gene sequencing instrument to work according to the sequencing flow control information. With the control device of the gene sequencing instrument provided by the embodiment of the invention adopted, a gene sequencing process can be greatly shortened, and the flux of the gene sequencing instrument can be improved.
