The protector is a key part of electric submersible pump (ESP), seals the motor and prevents the water entering into it. In order to solve the problem of complexity and uncertainty of fault propagation and analysis in protector, a new method for ESP protector fault diagnosis based on Fuzzy Petri nets (FPN) is proposed. Firstly, according to expert experiences and maintain rules, the FPN structure which has 28 places and 11 transitions is built to describe the protector fault propagation relations. Secondly, the five matrixes representing the FPN structure are obtained, and a rapid fault inference algorithm is designed via matrix operations. Finally, two fault diagnosis cases are analyzed, and the results show that the proposed method is valid and has strong engineering practicality.