The invention discloses a biomass-derived polyurethane nano composite emulsion and a preparation method thereof. The preparation method comprises the following steps: uniformly mixing and stirring dehydrated biomass-derived polyalcohol, a nano biological filler, a polyisocyanate monomer, a co-stabilizer and a catalyst in an ice water bath to obtain an oil phase; dissolving a surfactant in deionized water, and uniformly stirring in the ice water bath to obtain a water phase; mixing the oil phase and water phase, uniformly stirring in the ice water bath, and carrying out ultrasonic dispersion treatment to obtain a stable preemulsion; and heating the preemulsion to 60-90 DEG C, and stirring to react. The method utilizes the microemulsion polymerization process and characteristics thereof, abandons the nonrenewable petrochemical resource derived polyalcohol, introduces the renewable biomass polyalcohol and nano filler with wide sources and low price, and does not use any organic solvent, thereby achieving the goal of green raw materials and technique. The emulsion prepared by the method has the advantages of small particle size, high solid content, stable performance and long storage period.