Squeal noise often occurs in a two-stage electrohydraulic servo-valve, which is an unfavorable issue of modern hydraulic energy systems. The root causes of such noise from the servo-valve are still unclear. The objective of this paper is to explore the noise mechanism in a servo-valve excited by the pressure pulsations from the hydraulic energy system perspective. The suppressing capability of squeal noise energy is investigated by changing the pressure pulsation frequency and natural frequency of the flapper-armature assembly. The frequencies of the pressure pulsations are adjusted by setting different speeds of the hydraulic pump varying from 10,400-14,400 rpm, and two flapper-armature assemblies with different armature lengths are used in the tested hydraulic energy system. The first eight vibration mode shapes and natural frequencies of the flapper-armature assembly are obtained by numerical modal analysis using two different armature lengths. The characteristics of pressure pulsations at the pump outlet and in the chamber of the flapper-nozzle valve, armature vibration and noise are tested and compared with the natural frequencies of the flapper-armature assembly. The results reveal that the flapper-armature assembly vibrates and makes the noise with the same frequencies as the pressure pulsations inside the hydraulic energy system. Resonance appears when the frequency of the pressure pulsations coincides with the natural frequency of the flapper-armature assembly. Therefore, it can be concluded that the pressure pulsation energy from the power supply may excite the vibration of the flapper-armature assembly, which may consequently cause the squeal noise inside the servo-valve. It is verified by the numerical simulations and experiments that setting the pressure pulsation frequencies different from the natural frequencies of the flapper-armature assembly can suppress the resonance and squeal noise.