The microstructure of silicon nitride thin film prepared by ECR-PECVD is studied by transmission electron microscopy (TEM), scanning tunnel microscopy (STM) and PDS microphotometer. The results indicate that the Si3N4 thin film prepared by ECR-PECVD at lower temperature is the nano-Si3N4 thin film , the crystalline grain size lies between 14 to 29nm ,and this kind of Si3N4 thin film has fine surface planeness. We analyzed the mechanism of the formation of crystalline Si3N4 thin film at lower deposition temperature.