The invention relates to an automatic control system of a gas turbine generator set. The system adopts a plug-in board structure, and includes a main channel and a subsidiary channel. The main channel comprises a secondary power supply, a single chip microcomputer, an optical coupling input isolation circuit, a photovoltaic relay output isolation circuit, a data acquisition circuit, and an electromagnetic valve drive circuit. The subsidiary channel adopts a sequential logic circuit to realize the control function. The system provided by the invention completes cold start, process startup and programmed start by receiving external instructions, monitors the air inlet temperature, the exhaust temperature, the lubricating oil pressure, rotation speed and other over 30 operating parameters of the generator set during working, accomplishes over 20 fault protection and alarm functions, and transmits the exhaust temperature, the rotation speed, the fault and other information to a display control device, thus realizing the human-computer interaction function.