The shallow nitrogen-vacancy center of diamond exhibits excellent sensitivity and resolution in the magnetic detection and quantum sensing areas. Compared with other methods, low-energy carbon ion implantation does not need high-purity diamond nor introduce new impurity atoms, but the formation mechanism of nitrogen-vacancy center is not clear. In this work, shallow nitrogen-vacancy centers are created in the diamond by low energy carbon ion implantation and vacuum annealing, and the transformation mechanism of nitrogen-vacancy centers in diamond is studied by Raman spectroscopy, X-ray photoelectron spectroscopy, and positron annihilation analysis. The results show that shallow nitrogen-vacancy centers can be obtained by carbon ion implantation combined with vacuum annealing. After implantation, superficial layer of diamond shows the damage zone including lattice distortion and amorphous carbon, and carbon-vacancy cluster defects (carbon atoms are surrounded by vacancy clusters) are generated. In the vacuum annealing process, the damaged area gradually transforms into the diamond structure through the recovery of the distortion area and the solid-phase epitaxy of the amorphous carbon area, accompanied by the continuous dissociation of carbon-vacancy cluster defects. When samples are annealed at 850 and 900 ℃, the structure of the damaged area is partially repaired. While annealing at 950 ℃, not only the damaged layer is basically recovered, but also nitrogen atoms capture the single vacancy obtained by the dissociation of carbon vacancy clusters, forming the nitrogen-vacancy centers.