The invention provides a medical polyurethane thin film and a preparation method thereof. The polyurethane thin film comprises the following raw materials: polyurethane, polyethylene, polyethylene glycol, ultra-fine chitosan powder, dihexyl phthalate, 4,5-epoxytetrahydrophthalate, epoxidized soybean oil, polymethylphenyl siloxane fluid, calcium carbonate, N-cyclohexylethanolamine, triphenyl phosphite, 1,4-dioxane and N,N-dimethylformamide. The preparation method comprises the following steps: firstly feeding each component into a mixing stirrer, uniformly mixing and stirring, then adding an obtained mixed material into a reaction kettle, heating, performing stirring reaction, finally pouring an obtained film preparing liquid into one side of a glassine paper matrix, uniformly pushing the liquid to the other side by using a coating machine, putting a coated film preparing liquid and the matrix into clear water together, taking out after film forming, washing, drying, and stripping off from the matrix to obtain the medical polyurethane thin film. The medical polyurethane thin film provided by the invention has excellent mechanical performance, and also has a very good water vapor transmission rate.