Micropores in coal, which can be manipulated by aggregate structure, have been widely considered to be a key factor affecting the gas adsorption of coal. In this study, to explore the aggregate structure evolution and its influence on micropores during coalification, a well characterized sample set of medium-rank coals from Shanxi province, covering a vitrinite reflectance (Ro) interval from 0.68% to 1.98%, was selected. High resolution transmission electron microscopy (HRTEM) and low-pressure CO2 adsorption experiments (LPCO2) were employed to quantify the evolution of aggregate structure and micropores in coal during coalification. The results show that the two methods give similar results for the micropore distribution. With the increase of coalification, four obvious stages are found for fringe length and distribution of micropores, with turning points appear near Ro = 1.20% and 1.50%, respectively, indicating that the coalification process are combination of continuity and jumping and related to the coalification jumps. The dominant fringes are short fringes (0.3 ∼ 0.54 nm) and intermediate fringes (0.55 ∼ 1.14 nm) in all coals, which contribute most to the curvature of c = 1.0 ∼ 1.04 and c greater than 1.04, separately, suggesting the existence of non-six-membered rings. The curvature of c = 1.0 ∼ 1.04 decreases while the curvature of c = 1.04 ∼ 1.15 increases with increasing Ro, indicating that the fringes mainly tend to bend in medium-rank coals. For micropores, most pores in coal were found to be in the range of 0.5 ∼ 0.8 nm based on the result of HRTEM images, which mostly appeared in the disorder regions featured with intermediate fringes. However, the pores of 0.8 ∼ 1.2 nm and 0.4 ∼ 0.5 nm are always found in the regions without the basic structural units (BSUs) in lower-rank coals and the edge regions stacked with long fringes in the higher-rank coals, respectively. This work provides a strategy to manipulate micropores of medium-rank coal through aggregate structure evolution during coalification, which is expected to provide theoretical basis for further research on gas adsorption of coal.