Abstract Strike-slip fault zones are an important type of structure formed during continental orogenic events. Exploring the influence of strike-slip faults on the distribution of natural gas by using the 3D finite element method (FEM) is a frontier in the field of geoscience. In this paper, the effects of strike-slip faults on the heterogeneity of in situ stress and reservoir quality were systematically studied in a shallow commercial coalbed methane reservoir in the Shanxi Formation in the southern Qinshui Basin. Systematic 3D FEM modeling and in situ stress evaluation of a highly developed strike-slip fault zone were conducted. The results indicate that the simulated in situ stress distributions of σH, σh and σv in the target layer present ranges of 10–55 MPa, 3–23 MPa and 5–30 MPa, respectively, which are consistent with acoustic emission and hydraulic fracturing measurements. Along the strike-slip faults, the distribution of horizontal in situ stress is mainly affected by the fault length and vertical throw. The stress magnitude differs greatly between the two sides of a given strike-slip fault, affecting the compaction degree and petrophysical properties of the gas-bearing reservoir on both sides of the fault. Along the strike of a given strike-slip fault, the minimum horizontal in situ stress exhibits distinct segmentation characteristics, which affect the distribution of wells with a higher and lower yields. For the 2 s-order faults (the Sitou and Houchengyao faults), wells with a higher gas production capacity are typically located on the northwestern side of the faults. In the middle and southern sections of the Sitou-Houchengyao strike-slip fault zone, both highly concentrated faults and large-scale opening faults (basement and surface faults) produce greater stress concentrations, and the gas production capacity of the gas wells in these areas is poor. When the main strike direction of the faults is consistent with the loading direction of the boundary stress, the stress concentration is relatively low; whereas, the stress concentration increases as the angle between the main fault strike and the loading direction increases. The shear stress of the target layer is characterized by clockwise rotation, which is an important control on the stress heterogeneity of the strike-slip faults in the study area.