In recent years, the enterprises, as the main innovation subject in China, have made high achievements in the field of patent. The influencing factors of the patenting behavior in enterprises have caused the wide attention of many scholars at home and abroad. Based on the institutional theory, this paper focuses on the influencing factors of the patenting behavior in enterprises by the empirical research. The research results indicate that the internal factors are the main factors affecting the patenting behavior while the external factors are the secondary factors; and that the internal and external factors of the enterprises affect the patenting behavior through intermediary, namely the different motivations of employees. At last, this paper puts forward some suggestions for the patenting behavior in enterprises.