In order to reduce the distortion of acceleration vibration signal caused by the flow nonlinearity on electro-hydraulic servo shaking table, a control strategy based on the nonlinear compensation of flow is presented. Nonlinear flow equations of two valve cavities are built through the throttle equation. Combined with the hydraulic continuity equation and force balance equation, a nonlinear model of electro-hydraulic servo shaking table is established. According to the Taylor equation near the steady state point, the linear control model of the nonlinear hydraulic system is also given. Considering the maximum dynamic output force, a nonlinear compensation function related to the load pressure is introduced, which makes the flow of the compensated servo valve linearly with the spool displacement. The simulation and experimental results show that the nonlinear flow compensation control method can effectively reduce the acceleration distortion and improve the tracking accuracy of the vibration signal.