To investigate the factors of pore–fracture structure heterogeneity in middle rank coal reservoirs, middle rank coal samples collected from the deep coal seams in the northern part of the Kuqa area in the Tarim Basin are analyzed. Firstly, according to the maximum vitrinite reflectance (R_o,max), all the samples are divided into two types, Type A and B (A: R_o,max is larger than 1.2%; B: R_o,max is smaller than 1.2%). Secondly, the full-scale pore–fracture system was characterized using a combination of three experiments: high-pressure mercury intrusion testing, low-temperature CO₂ adsorption testing, and low-temperature nitrogen adsorption testing. Subsequently, multifractal theory was applied to evaluate pore structure heterogeneity and investigate its governing factors. The results are as follows: (1) Type A samples exhibit superior micropore development, whereas Type B samples show a higher degree of mesopore and macropore development. Both types of samples display a “bimodal” distribution across the full-scale pore. Type A pore structure is affected by R_o,max and macerals, with mineral components having a minor impact, while Type B is regulated by all three factors. (2) The coal samples exhibit distinct multifractal characteristics. Type A pore structure heterogeneity is higher than that of Type B. This heterogeneity in Type A is dominated by the differences in the development and distribution of small-scale pores (micro- and mesopores), whereas in Type B, it is governed by the full-scale pore system distribution.