The nano-graphite particles are preset on the silicon substrate and irradiated by 500 W fiber laser under the protection of argon gas. The micromorphology and crystal structure of transformation products after laser irradiation are studied with different laser energy densities. Transmission electron microscopy (TEM), Raman spectra and X-ray diffraction are used to analyze the micromorphology and crystallinity of transformation products. When the laser energy density reaches to 3.33 kJ/cm2, the particle sizes of the transformation products become bigger than that of the original. When the laser energy density reaches to 4.17 kJ/cm2, the linear morphology can be observed on the surface of samples. When the laser energy density reaches to 8.33 kJ/cm2, the original polycrystalline structures of transformation products is transformed into massy crystal structures. The results show that the laser energy density can significantly affect the micromorphology and crystal structure transformation of the nano-graphite particles on the silicon substrate.