Working under a wide range of conditions, especially extreme conditions, causes significant energy dissipation and thermal deformation that affect the micro-scale oil film clearances between the piston/cylinder interface of electro-hydrostatic actuator (EHA) pumps. This study aims to provide a tolerance design guideline for the piston/cylinder interface under a wide range of working conditions, including extreme speed, pressure, and temperature domains. The guideline is developed based on the comprehensive consideration of friction force and leakage and the constraint of sticking threshold through a Thermal-Fluid-Structure model. The optimized clearance is presented in the form of tolerance to account for realistic manufacturing precision. The accuracy of the optimal results is further validated through experiments.