The invention belongs to the technical field of fuel batteries, and relates to a PBI-based polysiloxane and phosphonic acid high-temperature proton exchange film and a preparation method thereof. The PBI-based polysiloxane and phosphonic acid high-temperature proton exchange film disclosed by the invention is prepared through the following method: dispersing polysiloxane and phosphonic acid in dimethylacetamide, and preparing to obtain a polysiloxane and phosphonic acid gel; then dissolving PBI in dimethylacetamide to obtain PBI polymer solution; then uniformly mixing the polysiloxane and phosphonic acid gel with the PBI polymer solution, then preparing by a tape-casting film-forming technique to obtain the PBI-based polysiloxane and phosphonic acid high-temperature proton exchange film. The doping amount of phosphonic acid is low and phosphonic acid is not liable to exude when the high-temperature proton exchange film prepared by the preparation method disclosed by the invention achieves a certain proton conductivity, and the high-temperature proton exchange film has a high proton conductivity under a high-temperature and low-humidity condition; moreover, the medium-temperature proton exchange film is good in flexibility, high in mechanical strength, and good in durability in a high-temperature fuel battery.