Two silane compounds, i.e., ((chloromethyl)phenylethyl)trimethoxysilane (Ph‐Si) and 3‐chloropropyltriethoxysilane (Pr‐Si), are employed as covalent crosslinkers to fabricate high temperature proton exchange membranes based on polybenzimidazole (PBI) in order to better understand the correlation between the structure and the property of the crosslinked membranes. All the crosslinked PBI membranes display longer morphology durability over the neat PBI membrane toward the radical oxidation. The crosslinked membranes with the crosslinker containing a rigid group of phenylene (PBI‐Ph) show superior acid doping level, high conductivity, and excellent mechanical strength simultaneously, comparing to those with the crosslinker having a flexible alkyl chain (PBI‐Pr) and the pristine PBI based membrane. The technical feasibility for using as high temperature proton exchange membranes is demonstrated by the acid doped crosslinked PBI‐Ph membranes via fuel cell tests.