Polyurethane microcapsules containing water-borne polyurethane (PU) paint as a core material for self-repairing protection coatings were successfully manufactured via interfacial polymerization of diol–diisocyanate prepolymer and 1,4-butanediol as a chain extender in an emulsion solution. The chemical structure of the resultant microcapsules was characterized by Fourier Transform Infrared Spectroscopy. Spherical capsules were observed with an average diameter of 39–72 μm and average shell thickness of 3.8–5.5 μm, while controlling agitation rates (2000–8000 rpm). The PU shell wall thickness was linearly proportional to the measured capsule diameter, thus, showing that the ratio of capsule wall thickness to diameter was constant (∼0.08). The typical core content and synthetic yield of the filled capsules were approximately 44–59 wt% and 31–67%, respectively. Thermal gravimetric analysis and scanning electron microscopy results support the determined thermal stability and morphology of the samples. Scratch tests, used to evaluate self-healing protection coating systems, showed that these materials had significant ability to recover from damage on the substrate, depending on the diameter and the concentration of the PU capsules in the paint layer, which could control the efficiency.