Fuel cell polymer membrane as the core of the proton exchange membrane fuel cell (PEMFC) plays an important role in maintaining high intrinsic proton conductivity and insulating electrode. To investigate the effect of crosslinking formation on proton conduction, the proton mobility and ion conduction were calculated and analyzed by using molecular dynamics (MD) simulation. As the crosslinking number increased, the proton diffusion coefficients increased at first and then decreased. The results indicated that the formation of crosslinked bonds was beneficial for opening new channels to enhance the proton conductivity. But too many crosslinking also can decrease proton diffusivity due to the blocking along the chain backbone. Besides, the proton conduction was better at 350 K than at 300 K. It can be concluded that temperature also had a significant impact on diffusivity and conductivity.