The invention provides a crosslinking composite organic phosphonate high-temperature proton exchange membrane and a preparation method thereof. Particularly, the invention provides the high-temperature proton exchange membrane which is formed by combining (a) a polybenzimidazole compound A; (b) an acid-alkaline organic phosphonate polymer B containing hydroxyl functional group or protected by hydroxyl protected group; and (c) a small molecule crosslinking C which are used as raw materials, wherein the mole ratio nA and nB of the A and B is 1:(0.01-99.99), and the acid-alkaline organic phosphonate polymer B is a copolymer formed by copolymerization of an alkaline olefin monomer D and an organic phosphonate monomer E. The crosslinking composite organic phosphonate high-temperature proton exchange membrane has high proton conductivity, high mechanical strength, high oxidization-resistant stability and low phosphonate wastage rate and is very suitably used for preparing the high-temperature proton exchange membrane fuel cell.