Abstract The assessment of coalbed methane (CBM) reservoirs can provide insights into the evolution of the pore structure systems around the first coalification jump (FCJ). The southern Junggar Basin, a typical low-rank coal-bearing basin in northwestern China, has been of interest to scientists and policy-makers due to its abundance of CBM resources and favourable conditions for CBM enrichment. A total of 28 coal samples from the Middle Jurassic Xishanyao Formation collected from 11 sampling sites in the central segment of the southern Junggar Basin were analyzed in this study. These samples were quantitatively characterized and comprehensively evaluated using macroscopic to nanometer-scale methods including macroscopic coal description, proximate analysis, vitrinite reflectance measurements, maceral analysis, low pressure nitrogen adsorption (LPNA), scanning electron microscopy (SEM), mercury intrusion porosimetry (MIP) and nuclear magnetic resonance (NMR). The results show that the Xishanyao low-rank coals are characterized by low moisture contents, low or low-medium ash yields (eastern and western parts), high volatile matter contents, moderate vitrinite contents, and high inertinite contents. The physical property of the Xishanyao coals generally displays heterogeneity, with the specific surface area, the total pore volume, the air permeability and the transverse relaxation time (T2) ranging from 0.116 to 15.983 m2/g, 0.461 × 10−3 to 13.37 × 10−3 cm3/g, 0.001 to 151.66 mD (0.987 × 10−6 to 0.149 μm2) and 1.44–174.22 ms, respectively. A new parameter, namely micropore volume proportion per unit nano-meter, is proposed. Micropore and transition pore volume per nm, specific surface area, total pore volume, DN1 and DN2 (LPNA fractal dimension) all first increase, then decrease and finally increase with rising coal rank, while the maximum and minimum values of the maximum vitrinite reflectance (Ro, max) occur at 0.58–0.59% and 0.65–0.66%. The boundary of Ro, max corresponding to the FCJ can be further defined from 0.5-0.6% to 0.58–0.59% based on the evolution of adsorption pore structures. Thus, pore structure parameters related to adsorption capacity are controlled predominantly by coal rank. In addition, tectonic deformation has a strong impact on seepage pore structure but only a slight impact on that of adsorption pore, which leads to an ambiguous correlation or a complex trend between mesopore, macropore content, DMIP (fractal dimension of MIP) and coal rank around the FCJ. This study reveals the complex variation of pore structure evolution of low-rank coals and the significant influence of the FCJ on physical properties of coalbed methane reservoirs.