With the development of DC distribution system within the isolated power system of a ship or an aircraft, more constant frequency loads will be supplied by inverters connected to DC main bus. In the operating mode conversion process of an isolated power system, inverters will inevitably suffer from serious disturbance and affect the stability of the system. Therefore, it is important to establish a model of the inverter that reflects its dynamic characteristics and based on which to conduct the stability analysis. This paper proposes a 12-pulse inverter model based on the generalized state space averaging (GSSA) method. This model can overcome the limitations of 12-pulse inverter state space averaging (SSA) model in transient analysis with good accuracy and fast analysis ability effectively. Three kinds of models for a 12-pulse aircraft inverter are built in MATLAB, namely GSSA model, SSA model and detail device model. The simulation results show the high accuracy of GSSA model in stability analysis. This study provides an effective analytical tool for stability analysis of 12-pulse inverter and also provides a reference for inverter modeling research of isolated power system such as in aircraft or ship.