The leakage of the pilot stage of the 2D valve mainly depends on the size of its initial opening. According to the Routh criterion, the pilot stage of the two-dimensional magnetically levitated servo-proportional valve (2D-MSP valve) needs to be designed to have certain positive values to increase the damping ratio to improve valve stability, which leads to the leakage flow representing a non-negligible power loss. In order to reduce leakage flow and achieve goal of energy saving, this paper presents a novel resonance stability criterion by considering nonlinear characteristics of the fluid dynamic system. First, the 2D-MSP valve is regarded as a three-way valve-controlled differential cylinder system. Based on the frequency response of the resonance state, the energy conservation method is used to solve the flow “backfilling” area, the motion equation of the cylinder piston (valve spool displacement) and the pressure waveform of the sensing chamber under different opening and pressure amplitude ratio. Then, the analytical expression of the resonance peak amplitude is obtained and the resonance stability criterion is deduced. The result is compared with the Routh stability criterion, which illustrates that the positive openings of the pilot stage can be reduced to one-third of the original value. The prototype valve is then designed and manufactured based on the resonance stability criterion. The dynamic and static characteristics under different system pressures are measured. Experimental results show that the prototype valve is an over-damped system without any overshoot, which has excellent working stability, and its static and dynamic performance can meet the demands of the industry servo-proportional control system. The research work validates the effectiveness of the proposed resonance stability criterion.