The invention relates to a polyurethane (PU) on rust paint with a self-repairing function and a preparation method thereof, belonging to the technical field of paints. The PU on rust paint is formed by synthetic resin, molecular sieves, pigments, auxiliaries, solvents, fillers, a curing agent and the like. The preparation method is characterized by firstly synthesizing aluminium phosphate molecular sieves, secondly modifying the aluminium phosphate molecular sieves with an organic acid and an inorganic acid, thirdly enveloping the aluminium phosphate molecular sieves with coupling agents, and finally preparing the PU on rust paint with the enveloped aluminium phosphate molecular sieves. The paint has controllable rust layer transforming capability and good rustless iron-steel substrate self-repairing capability, and can be widely applied to on rust coating of transmission equipment, bridges, ships, offshore platforms, port facilities, outer walls of oil tanks and the like.