Aiming at the phenomenon of pressure pulsation at the outlet of the main fuel control system of an aeroengine, this paper systematically analyzes the reasons for the pulsation of the hydraulic system, lists the fault tree of the pressure pulsation of the main fuel control system of an aeroengine, and completes the fault location. The steady-state hydrodynamic force and associated parameters of the irregular opening fuel return valve under fault conditions are primarily investigated through flow field simulation, and it is noted that the theoretical formula is not applicable to the steady-state hydrodynamic calculation of the irregular opening valve and the change of the outlet jet angle. Then the transfer function and Simulink simulation model of the constant differential pressure module are established by small deviation linearization at the steady point, and its natural frequency and main influencing factors are studied. The findings demonstrate that the fuel pressure pulsation is caused by the return valve’s resonance under external stimulation, and the steady-state hydrodynamic force acting on the valve core is the primary factor influencing the return valve’s natural frequency. Through the study of the irregular opening shape of the valve, the fault improvement measures are given, which provide theoretical support for the optimal design of the system.