Graphite microcrystals are the product of coal graphitization and widely exist in the graphitized coal of Yongan Coalfield, Fujian Province, China, which is direct mineralogical evidence for the transformation of coal to graphite. Optical microscopy, scanning electron microscopy (SEM) and micro-Raman spectroscopy were used to detect the morphology and microstructure of the in situ graphite microcrystals. The results show that the volume proportion of graphite microcrystals in graphitized coal samples is between 2.39% and 7.32%, and the optical anisotropy of graphite microcrystals is stronger than that of coal macerals. Graphite microcrystals show the occurrence of attached microcrack inner walls or infilling the cell cavity, with several forms of flakes, needles or aggregates. Under optical microscopy of polarized light and with a retarder plate of 1λ, graphite microcrystals show the color of primary yellow and secondary blue, and the two kinds of colors appear alternately when the microscope is rotating. Additionally, flake-like graphite microcrystals with an isochromatic zone diameter of 10−50 μm are the most widely distributed in graphitized coal. Under SEM, graphite microcrystals show a rough and irregular edge and are characterized by flow or bubble film structures along with several pores, which is the product of cooling crystallization after the softening and melting of carbon-containing substances. Moreover, flake-like graphite microcrystals developed interlayer pores with a clear outline of loose stacking and were almost entirely composed of pure carbon; a small amount of oxygen is related to oxygen-containing functional groups or structural defects. The micro-Raman spectra of graphite microcrystals in the first-order region are characterized by low-intensity D1 and D2 bands and a high-intensity G band, and the parameters R1 and R2 vary from 0.21–0.39 and 0.60–0.74, respectively. The second-order micro-Raman spectra of graphite microcrystals are characterized by a higher intensity of the 2D1 band and a lower intensity of the other three bands. The parameter R3, derived from the area ratio of the 2D1 band to all the bands in the second-order region, was proposed. The value of R3 ranges between 0.78 and 0.86, and both of them indicate a higher percentage of graphene plane with a highly internal crystallographic structure. Similar to the parameters R1 and R2 in the first-order micro-Raman spectrum, the parameter R3 is an effective parameter to characterize the ordering degree of the microstructure, which may be used to evaluate the graphitization degree of graphitization coal.