A transmission control system for controlling a transmission. The system has a main transmission with a speed changing mechanism and an output shaft, a substransmission connected to the output shaft, and a control system for receiving outputs from a number of sensors which sense the running state of the vehicle. The control system itself has two outputs, there being two separate hydraulic controls connected to the two system outputs, respectively. The two hydraulic controls control the speed changing mechanisms of the main and subtransmissions, respectively. Also provided is a hydraulic pressure source which supplies a working fluid to the two hydraulic controls. The control system determines whether the main and subtransmissions are in a transient period of the speed changing operation and, as long as one of the two transmissions is in the transient period, inhibits the speed changing operation of the other transmission.