The electro-hydrostatic actuator (EHA) is one of the most prevalent types of power-by-wire (PBW) actuation systems. With the increase in EHA power density, using the pump’s leakage oil to cool the motor has been gradually adopted to solve the problem of excessive motor temperature. However, the viscous friction loss caused by the liquid viscosity will seriously affect the heat dissipation effect and dynamic performance of the motor. To calculate the motor viscosity loss accurately, a novel calculation method is proposed in this paper. Using the energy gradient theory, the relationship between the fluid flow state and the rotation speed is analyzed. In addition, the lumped parameter model of viscous loss is established by using the conservation of momentum theory and computational fluid dynamics (CFD) simulation. A test rig is designed to test the viscous friction loss for various rotation speeds, and the test results show a good agreement with the theoretical analysis. The present results demonstrate the effectiveness of the lumped parameter model and provide a better calculation method for wet motor viscosity loss calculation.