The invention discloses a preparation method of polyurethane prepolymer with low free isocyanate monomer. The preparation method comprises the following steps of: forming into mixed alcohol by trihydric alcohol and dihydric alcohol under the temperature of 120-150DEG C, and carrying out vacuum dehydration; putting isocyanate monomer and ester solvents into a reactor to keep the temperature at 30-70DEG C, and dropwise adding the mixed alcohol into the reactor; after dropwise adding, continuously reacting for 3-6h under the temperature of 40-70DEG C under stirring, and discharging in a cooling way to obtain polyurethane prepolymer; and separating the obtained polyurethane prepolymer, and adjusting the solid content of polyurethane prepolymer solid and the content of free isocyanate monomer in the separated heavy components by diluted solvent. According to the preparation method, the real continuous production can be realized, all the recovered solvent and isocyanate monomer can be recycled, the zero emission can be realized, and the real clean production can be realized; and the product has the characteristics of being low in viscosity, high and adjustable in NCO value content, low in the content of the free isocyanate monomer, high in solid content, good in compatibility, etc.