Micron-sized coatings prepared using physical vapor deposition (PVD) technology can peel off in extreme environments because of their low adhesion. Laser micro-melting (LMM) technology can improve the properties of the fabricated integrated material due to its metallurgical combinations. However, the microstructural changes induced by the high-energy laser beam during the LMM process have not been investigated. In this study, we used the PVD–LMM technique to prepare NiCr coatings with a controlled thickness. The microstructural changes in the NiCr alloy coatings during melting and cooling crystallization were analyzed using molecular dynamics simulations. The simulation results demonstrated that the transition range of the atoms in the LMM process fluctuated synchronously with the temperature, and the hexagonal close-packed (HCP) structure increased. After the cooling crystallization, the perfect dislocations of the face-centered cubic (FCC) structure decreased significantly. The dislocation lines were mainly 1/6 <112> imperfect dislocations, and the dislocation density increased by 107.7%. The dislocations in the twinning region were affected by the twin boundaries and slip surfaces. They were plugged in their vicinity, resulting in a considerably higher dislocation density than in the other regions, and the material hardness increased significantly. This new technique may be important for the technological improvement of protective coatings on Zr alloy surfaces.