A zero phase difference jumping compensation processing method for heterodyne interferometric signal processing based on pulse counting is proposed, which can guarantee the correction integration of measured integer and fraction phase. The integer phase measurement is realized by counting pulse numbers of two interference signals and synchronously subtracting. The fraction phase measurement is realized by frequency mixing and frequency reduction to improve the measurement resolution. A dynamic base signal is generated by tracking the reference interference signal with phase-locked loop and the signal is used for frequency mixing to solve the problem of frequency changing of heterodyne interference signals. This method can improve the resolution stability of fraction phase measurement. The verification experiments are done with a function generator，including phase measurement precision, integer counting and fraction phase measurement. A two-pass heterodyne interferometric optical layout is constructed for displacement measurement experiments, the displacements of precision stages are measured to verify the effectiveness of the proposed compensation method for integration of integer and fraction and the feasibility of the implemented signal processing method in actual heterodyne interferometric displacement measurement.