Deep low-rank coalbed methane (CBM) resources are numerous and widely distributed in China, although their exploration remains in its infancy. In this work, gas adsorption (N2/CO2), mercury intrusion porosimetry, and 3D CT reconstruction were performed on five coal samples of deep and shallow low-rank coal from northeast China to analyze their pore structure. The impact of the features in the pore structure at full scale on the capacity for methane adsorption and seepage is discussed. The results indicate that there are significant differences between deep low-rank coal and shallow low-rank coal in terms of porosity, permeability, composition, and adsorption capacity. The full-scale pore distribution was dispersed over a broad range and exhibited a multi-peak distribution, with the majority of the peak concentrations occurring between 0.45–0.7 nm and 3–4 nm. Mesopores are prevalent in shallow coal rock, whereas micropores are the most numerous in deep coal rock. The primary contributors to the specific surface area of both deep and superficial coal rock are micropores. Three-dimensional CT reconstruction can characterize pores with pore size greater than 1 μm, while the dominating equivalent pore diameters (Deq) range from 1 to 10 μm. More mini-scale pores and fissures are observed in deep coal rock, while shallow coal rock processes greater total and connection porosity. Multifractal features are prevalent in the fractal qualities of all the numbered samples. An enhancement in pore structure heterogeneity occurs with increasing pore size. The pore structure of deep coal rock is more heterogeneous. Furthermore, methane adsorption capacity is favorably connected with D1 (0.4 nm < pore diameter ≤ 2 nm), D2 (2 nm < pore diameter ≤ 5 nm), micropore volume, and specific surface area and negatively correlated with D3 (5 nm < pore diameter ≤ 50 nm), showing that methane adsorption capability is primarily controlled by micropores and mesopores. Methane seepage capacity is favorably connected with the pore volume and connected porosity of macropores and negatively correlated with D4 (pore diameter > 50 nm), indicating that the macropores are the primary factor influencing methane seepage capacity.