In view of the non-stationary characteristics of test signal caused by the complex structure, multi excitation sources and unstable running speed of reciprocating mechanisms, a fault diagnosis method of reciprocating mechanical system was proposed based on the generalized phase information. Taking the working period of a selected part as the reference standard, the working state signals of each part were uniformly calibrated, and the movement order characteristics of parts were reflected with the generalized phase difference. The effectiveness of the proposed method was verified by a typical fault diagnosis of discontinuous moving of the swing arm of reciprocating mechanism.