Addressing the leakage rate prediction problem of the PEMFC sealing system is of great importance for its stable operation. The leakage calculation method of the PEMFC sealing system is proposed based on thermal coupling. The parallel plate leakage model is improved to make it applicable to the leakage rate calculation with a variable channel cross-section height. The interface macroscopic contact pressure is solved using a finite element simulation for solid mechanics analysis. The Greenwood–Williamson model is used for contact mechanics analysis to solve for the average height of the leakage channel. The effects of the ambient temperature, compression ratio, bipolar plate misalignment, and gasket size on the cell sealing effect were studied numerically. The data indicated that as the ambient temperature, compression ratio, and gasket size became larger, the volume leakage rate began to be reduced. The leakage rate as a parameter to characterize the sealing performance, considering the influence of gasket size, operating conditions, and other factors on the cell sealing effect, is more meaningful for the durability study and failure analysis of PEMFC.