The invention discloses a method for modifying a waterborne polyurethane emulsion by cationic nano-cellulose. The method specifically comprises the following implementation steps: (1) uniformly dispersing the nano-cellulose into water, so as to form a nano-cellulose dispersion solution; (2) separately weighing a cationic ammonium salt and an alkaline solution according to the mass of the nano-cellulose dispersion solution obtained in the step (1); adding the weighed cationic ammonium salt and the weighed alkaline solution into the nano-cellulose dispersion solution, and carrying out a reaction, so as to obtain a product; and subjecting the product to centrifugation and in-water dialysis sequentially, so as to obtain a cationic nano-cellulose dispersion solution; and (3) uniformly mixing the cationic nano-cellulose dispersion solution obtained in the step (2) with waterborne polyurethane, thereby obtaining the stable cationic nano-cellulose modified waterborne polyurethane emulsion. According to the method for modifying the waterborne polyurethane emulsion by the cationic nano-cellulose, disclosed by the invention, the modified waterborne polyurethane emulsion can have good mechanical properties, water resistance and thermal stability.