The changes in the shape of micro-photoluminescence spectra of PECVD diamond micro-crystal measured, depending on the position of the excitation laser spot along the crystallite height, were analyzed. It was ascertained that the processes of SiV defect formation non-monotonically depend on the distance from the Si substrate. At the distances of 2–20 μm the concentration of SiV defects increases, then at distances larger than 20 μm the number of SiV defects decreases. The concentration of NV− and NV0 defects monotonically increases with the distance from the Si substrate. The predomination of SiV defect formation at the beginning stages of the crystal growth is explained by the substantial concentration of carbon vacancies required for their formation. With the increase in the distance from the substrate, the crystalline perfection increases, the concentration of carbon vacancies decreases and the processes of NV− and NV0 defect formation dominate. The increase in CH4 fraction within 0.75–6 % leads to the increase in the volume fraction of graphite-like carbon, which is the good diffusion channel for Si atoms from the substrate into the plasma. Therefore, the concentration of SiV, NV−, and NV0 defects on the surface of the crystal depends on the volume fraction of graphite-like carbon defined by CH4 content.