Hydraulic system is widely used as a power source in deep-sea operation equipment. The sealing performance and the relative movement of the parts in hydraulic components are significantly affected by the structural deformation at the clearance fit and the viscosity increase of the hydraulic fluid medium, which are both caused by high seawater pressure. In this paper, the deformation formula at the clearance fit in the deep-sea environment is deduced, which indicates that the deformed height of the fit clearance decreases linearly in the axial direction. A minimum clearance design criterion is proposed, and it is found that the smaller the difference between the bulk modulus of the matching parts and the fit radius are, the smaller the variation of the height of the fit clearance is under various working conditions and the smaller the required minimum initial height is. The leakage flow rate formula at the clearance fit in the deep-sea environment is deduced as well, which introduces modified factors to consider the effects of structural deformation, viscosity increase, and eccentricity. The calculation result shows that under the condition of 11 000 m deep sea, the leakage flow rate calculated by the classic formula is about five times larger than that of the modified formula. Multi-parameter fluid–solid-interaction simulations are carried out to verify the correctness of the deduced deformation and leakage flow rate formulas. The leakage flow rate of the situation with inclination involved is also analyzed through numerical simulations.