Micropores (< 2 nm) play an important role in coalbed methane adsorption, desorption, and diffusion. However, the mechanisms of micropore formation and evolution still need further study. This study primarily focuses on molecular structure controls on micropore evolution during coalification. CO2 adsorption experiments were employed to characterize micropore structure in coals, and C-13 nuclear magnetic resonance (C-13 NMR) and X-ray diffraction (XRD) were employed to characterize the molecular structures of those coal samples. The results demonstrated that micropore evolution during laboratory simulated coalification was similar to that in geo-time-scale natural maturation. This suggests that laboratory simulated coalification can be an effective method for studying micropore evolution during coalification. Micropore evolution in laboratory simulated coalification and natural maturation both exhibited a parabolic curvature with coal rank, with a minimum at similar to 1.4%. When vitrinite reflectance (R-o) was < 1.4%, micropores were mainly controlled by the aliphatic part of the coal samples, and micropore volume decreased with decreasing aliphatic functional groups. When R-o varied from 1.4% to 4.0%, micropore structure was mainly controlled by aromatic parts and coal crystallite structure. In this coalification stage, micropore volume showed linear correlation with the fraction of aromatic bridgehead carbon, the fraction of protonated aromatic carbon, and the ratio of aromatic bridge carbon to aromatic peripheral carbon (X-BP). Moreover, the increase in lateral sizes (L-a) and the decrease in interlayer spacing (d(002)) both resulted in the increase in micropore volume. In conclusion, the coal microporosity and its evolution were primarily determined by coal molecular structure. In different coalification stages, microporosity and its evolution were controlled by different sub-portions of the whole molecular structure. These findings can provide mechanistic insights of gas sorption and diffusion, as gas sorption and diffusion behaviors are simultaneously controlled by both pore structure and molecular structure.