The invention discloses a preparation method of waterborne polyurethane with excellent freeze-thawing stability. The preparation method specifically comprises the steps of: at 20-80 DEG C, adding amino type polyhedral oligomeric silsesquioxane into acetone of excessive isocyanate monomer, reacting to be clear, setting the temperature to be 60 DEG C, adding ethyoxyl-terminated polymer glycol, diol and polyol, and catalyst di-n-butyl tin dilaurate, reacting for one to two hours, and controlling the R value to be 1.50-3.00 in the prepolymerization reaction; then increasing the temperature to be 70-90 DEG C, continuously reacting for one to two hours, then cooling to room temperature, adding water for dispersion, adding a chain extender at 30-50 DEG C to conduct chain extension reaction for two to four hours, and cooling to room temperature to obtain waterborne polyurethane. Through tests, the waterborne polyurethane has favorable wear resistance property and bonding strength, as well as excellent freeze-thawing stability.