Abstract: Gas-cooled micro reactor (referred to as "micro-reactor"), as a micro-nuclear power source, can provide reliable power supply for the micro-grid in remote areas. Because of the characteristics of small output power and remote construction location, and considering the economic impact, it is necessary to reduce the personnel intervention as much as possible to improve the automatic operation capability of the gas-cooled micro reactor. Therefore, it needs to vigorously carry out research on the automatic operation of the gas-cooled micro reactor. The application of automatic startup and shutdown control system (APS) is a key technology to realize the automatic operation. This paper introduces the design method for the automatic startup and shutdown operation of gas-cooled micro reactor. Based on the system design and characteristics of micro reactor, firstly, the startup and shutdown processes are analyzed, then APS design and sequential control logic model construction are carried out, and finally the APS design scheme of the micro reactor is simulated and verified. The verification results show that for the implementation of APS logic in startup and shutdown processes, the change curves of important parameters are in line with the expected results of logic. Therefore, the design method of automatic startup and shutdown of micro reactor proposed in this paper is effective and feasible.