Magmatic intrusion into coal-bearing sequences can significantly affect the rank of the intruded coal and change the macromolecular and pore structures. Here, we use Raman microscope and Atomic force microscope (AFM) to obtain quantitative information on these transformations. Six coal samples of different ranks taken from a magmatic intrusion zone of Huainan Coalfield, China, were studied. The Raman spectra were fitted with a combination of 8 Lorentzian bands and 1 Gaussian band. We found that the macromolecular structures in coals of different ranks have significant relationships with Raman spectral parameters, particularly the band area ratios (I-D1/I-G, I-D2/I-G, I-D3/I-G, I-D4/I-G and I-G/I-All). With the increase of coal rank, I-D1/I-G, I-D2/I-G, I-D3/I-G and I-D4/I-G show trends of decreasing intensity, suggesting an enhanced orientation of aromatic hydrocarbons. Observations by Atomic force microscopy indicate that the pore parameters (e. g. amount, size, shape) are quite different for different ranks of coals. The pore size of low-rank bituminous coal is much larger than high-rank anthracite and pore abundance is higher in the former. In addition, there is also good correspondence between the surface topography of coal grains and coal rank.