Laser micromelting (LMM) technology allows for the remelting of pre-positioned coatings on the surface of a specimen to form a metallurgical bond with the substrate material, significantly improving the coating’s film–base bond. However, the high energy input from the laser modification process can cause severe element diffusion, rendering the coating susceptible to deformation and cracking. This can be mitigated by controlling the laser power, scanning speed, and offset of the LMM process. The temperature and stress fields of the samples in the LMM process were analyzed via finite element simulation. The effects of the LMM process parameters on the coating morphology were analyzed in conjunction with experiments. The results indicated that the laser power significantly affected the morphology of the coating after remelting, and a higher scanning speed was more likely to cause the coating to accumulate stress. Additionally, a smaller offset inhibited crack generation. At a laser power of 30 W, a scanning speed of 1200 mm/min, and a scanning spacing of 0.035 mm, the surface of the coating had no obvious defects and was relatively flat, and the adhesion and corrosion resistance were significantly improved. This study provides valuable guidance for improving the preparation of micron-sized protective coatings on Zr alloy surfaces.