The dynamic performance and load capacity of a deep-sea electric manipulator are obviously affected by the viscous resistance of compensating oil. However, the complex geometric clearance of the oil-filled joint of the manipulator makes it difficult for existing theoretical models to accurately model this problem. Based on the existing theoretical models, a viscous power model considering the influence of the surface grooves of the rotor and stator is proposed. To reduce the viscous power loss, an optimization method for the clearance geometry is proposed. This optimization method is carried out by filling the surface grooves of the motor rotor and stator with epoxy resin. This method makes the clearance geometry of the compensated oil more regular. The modified model and optimization method are validated by designing an experimental installation and method. The experimental results demonstrate the accuracy and effectiveness of the modified theoretical model and optimization method.