The invention discloses an FCT test system with multiple test stations controlled by one computer. The FCT test system comprises the computer, n test stations, a communication gathering and distributing device, a router, a code scanning station, a circuit board motion control device and an OK/NG board receiver. The control method of the FCT test system comprises the following steps: S1, detecting a to-be-tested circuit board; s2, issuing a code scanning instruction; s3, uploading a code scanning instruction; s4, judging whether code scanning succeeds or not; s5, transmitting the circuit board and preparing for testing; s6, judging whether the program is downloaded or not; s7, judging whether the program is successfully downloaded or not; s8, testing the circuit board; and S9, receiving the qualified circuit board. According to the testing system and method, multiple computers do not need to be operated at the same time, only one computer needs to be operated, only one upper computer program runs on one computer, the system design is simplified, the hardware cost is reduced, meanwhile, the operation process is simplified, and the error probability of operators is reduced.