Proton exchange membrane (PEM) fuel cell is widely recognized as an outstanding portable power plant and expected to be possibly commercialization in the near future. As is well known, mechanical stresses implemented on the bipolar plates during the assembly procedure should have prominent influences on mass and heat transfer behavior inside the cell, as well as the resultant performance. In this study, an analytical model is proposed to comprehensively investigate the influence of clamping force on the mass transport, electrochemical properties and overall cell output capability of a PEM fuel cell. The results indicate that proper clamping force not only benefits the gas leakage prevention but also increases the contact area between the neighboring components to decrease the contact ohmic resistance. However, deformation always takes place simultaneously, changing the local physical structures of the cell components, which possibly leads to the decrement of porosity and permeability of the gas diffusion layer (GDL) and catalyst layer (CL), hinders the gas species and liquid water transport in GDL, and also decreases the cross-sectional flow area in the channel. The combined effect of the aforementioned factors finally contributes to the cell performance fluctuation. Moreover, although the contact resistance decreases with increasing stresses, more significant mass transfer losses, e.g. lower membrane water content and larger gradient in liquid saturation, results in more serious concentration voltage losses and weaker proton conductivity in the membrane, further impairing the cell voltage output. Therefore, cell performance should be optimized by the balancing among the transport properties and the contact resistance involved in the fuel cell. By using this analytical model, optimal cell design parameters and clamping pressure exerted on the fuel cell can be quickly predicted accordingly. Proper discussions are carried out and suggestions are proposed.