Poly(urea-formaldehyde) (PUF) microcapsules were prepared by in-situ polymerization with four different processes in this paper. The chemical composition, surface morphology, particle size distribution, and thermal stability were characterized by FTIR, SEM, particle size analyzer, and TGA, respectively. The results demonstrated that the agglomeration of the PUF microcapsules was related to the agglomeration of the emulsion particles caused by the changes of emulsion interface during the shell polymerization. Due to the slow deposition of the shell material, the PUF microcapsules with the core-shell structure prepared by the process with ammonium chloride as the last additive showed good dispersibility with an average diameter of 6.36 μm, high core content of 71.3 wt%, and high yield of 61.3 wt%. The PUF microcapsules had good thermal stability below 216C. The PUF microcapsules could be uniformly dispersed in the epoxy coating in a single form. The epoxy coating with 2 wt% PUF microcapsules showed good self-healing property, and the service life of the coating was about doubled.