This paper presents an early fault diagnosis method for the high-pressure diaphragm pump check valve based on the differential empirical mode decomposition. First, the differential transformation of the vibration signals is derived to increase the amplitude ratio of the high-frequency component for easy extraction in the subsequent decomposition. Further, empirical mode decomposed (EMD) is applied on the signals and the intrinsic mode functions obtained from EMD are restored by integral. Finally, the components with smaller K-L divergence with the original signals is selected to reconstruct, and the instantaneous frequency spectrum of reconstructed signals is analyzed by Hilbert marginal spectrum to extract the characteristics of the fault vibration signals. Simulation and engineering experimental analysis show that the proposed method can extract the fault feature information better.