The invention discloses a preparation method of waterborne flame-retardant self-repairing polyurethane based on modified graphene. The method comprises the following steps: firstly, ultrasonically crushing amino cyclotriphosphazene and isocyanate silane covalently modified graphene oxide, then reacting with macromolecular diol, a hydrophilic chain extender and diisocyanate, terminating with diselenide diol, neutralizing, emulsifying, and adding waterborne self-repairing polyurethane containing diselenide bonds so as to obtain the waterborne flame-retardant self-repairing polyurethane emulsion. According to the invention, by reducing the size of graphene oxide and modifying a waterborne polyurethane chain, the water dispersion stability and the dispersion uniformity and compatibility of the graphene oxide in the membrane are improved, so that the mechanical strength of the membrane is improved; due to nitrogen phosphorus silicon modification, the flame retardant property is further improved; the material is endowed with a good room-temperature illumination self-repairing function through double selenium bonds; and the method provided by the invention is environment-friendly, and the prepared material has high mechanical property and excellent flame-retardant self-repairing function, and can be applied to various fields of leather finishing, fabric finishing and the like.