Abstract: Based on an independently developed large-scale parallel code NEPTUNE3D, a module of electromagnetic field finite-difference-time-domain method coupled with a plasma fluid model is programmed and built to investigate the physical phenomena of high power microwave (HPM) flashover and breakdown on the inner surface of the output window. By using improved NEPTUNE3D code, the 1.3 GHz HPM flashover and breakdown on the inner surface of the output window are simulated. The numerical results indicate that the plasma shape formed in flashover and breakdown is relevant to the initial seed electron distribution type. For the point source central distribution, the developing plasma configuration is like a mushroom; the shortening of the output microwave caused by plasma absorption is not serious. For the face-source distribution, the developing plasma configuration is like a hat; the shortening of the output microwave is intense, the plasma absorption effect is dominant at the initial stage, while the plasma reflection effect dominates when the plasma density is up to a high enough value. The output microwave pulse width could be prolonged by decreasing the microwave power, the outgassing rate and the initial seed electron density, respectively. The outgassing depth barely affects the width of the shortened microwave output pulse.