The graphitization of coal is complicated due to multiple factors, such as magmatic intrusions, tectonic stresses and the catalysis of minerals. Heterogeneous graphitization was found based on the nanostructural characterization of anthracite and coal-based graphite. It was determined that the graphitization of coal is not only the rearrangement of carbon layers but also the extinction of structural defects, as revealed by the evolution of XRD and Raman spectra and structural parameters (i.e., the interlayer spacing d002 and R2). Based on a comprehensive analysis of the nonstructural evolution of coal, the graphitization of coal could be divided into four stages at the nanoscale. The first stage (d002 > 0.344 nm and R2 < 0.7) is the transition process from coalification to graphitization, the second (0.337 nm < d002 ≤ 0.344 nm and R2 > 0.65) is the crystallization of carbon layers, the third stage (0.337 nm < d002 ≤ 0.344 nm and R2 ≤ 0.65) is characterized by the elimination of structural defects and straightness of carbon layers, and the fourth stage (d002 ≤ 0.337 nm and R2 ≤ 0.6) shows that the locally ordered graphite structure expanded to the whole sample.