With the increase of mining depth, the complex burial conditions enhance the chemical and physical heterogeneity of deep-burial coal. The accurate characterization of the nanopore within deep-burial coals is still a challenge. In this work, atomic force microscopy (AFM) measurement was conducted on 12 deep-burial coal samples with different ranks varying from bituminous C to anthracite, attempting to gain clearer insights into the nanopore characteristics and surface roughness. Based on the 3-D surface topographies by AFM, nanopore parameters were determined through image processing and analysis. Quantitative study has been carried out on coal surface roughness. Besides, the validation and limitation of AFM experiment were also analyzed, and the correlations between these nanopore parameters and coal rank (indicated by vitrinite reflectance, R-o) were established. The results show that the mean pore size of studied coal samples ranges from 6.83 nm to 40.16 nm with the areal porosity of 0.65%-9.76%. AFM images indicate that the macromolecular of lower rank coals (bituminous C) is arranged loosely with abundant larger pores, but the anthracite molecular is more ordered with regular network structures. A U-shape curve relationship with the bottom at R-o approximately 1.25% has been found between both the nanopore number and areal porosity with increasing R-o, demonstrating two evolution stages. The values of surface roughness parameters R-a and R-q are 6.43-30.27 nm and 7.51-35.27 nm, respectively. The exponential decline of surface roughness with increasing coal rank suggests that coalification enables coal surface to become smooth. Comparison of nanopore size distribution explored by AFM and lowpressure nitrogen gas adsorption (LP-N(2)GA) has also been made, indicating that AFM is an effective tool for coal nanopore characterization.