From viewpoints of energy saving and environmental problem, we have developed marine waste hear recovery systems used Stirling engine generators. The engine system keeps safety operation with an engine speed control system by an inverter. On the other hand, when the system has unexpected condition, such as interception of electric load or a trip of the inverter, the engine needs to stop speedy and safety, because the over speed of the engine may bring destruction of the engine mechanism or electrical fires. In this paper, we discuss shutdown methods for a Stirling engine generator, and show test results of a 500 W class Stirling engine generator to investigate effects of shutdown method with connecting pipe between the working space and the buffer space.