The theory of shallow coalbed methane (CBM) exploration and development cannot be directly applied to deep CBM partly due to the effect of in situ stress. In situ stress in deep coal beds restricts the process of CBM adsorption/desorption and seepage, determines the effectiveness of coalbed fissures, and affects the design of horizontal well trajectory. Thus the pattern of in situ-stress change in deep coal seams is of great significance to the exploration and development of CBM. In this paper, taking the Daji block in Ordos Basin as an example, using data from array acoustic logging, microseismic monitoring, and core testing, considering the microstructure types and attitude, boundary stress conditions, and combination of mechanical properties of top and bottom slabs, we established a three-dimensional geomechanical microstructural model of deep coal beds by using ANSYS finite element software to comprehensively analyze the control mechanism of microstructure types and attitute on in situ stress in deep coal beds. Results show that with smoother microstructure the stress distributes more uniformly; conversely, the stress concentrates more easily. The influence of the attitute of microstructure on in situ stress in coal seams is mainly as follows: as the curvature of the microstructure increases, the differential horizontal stress at the bending point increases, and the minimum principal stress increasingly concentrates around the bending point. According to cross-simulation between microstructure type and mechanical properties of coal seam, lithology of top/bottom slabs, and boundary stress conditions, in situ stress under positive curvature is positively correlated with Poisson’s ratio and negatively correlated with Young’s modulus, whereas the opposite is true under negative curvature. Compared to with sandstone top slab, the magnitute of in situ stress in coal seams with limestone top slab is more significantly affected by the change of microstructure type. The magnitude of the regional stress has relatively small influence on in situ stress in deep coal seams. The research results provide an useful reference for the genetic analysis of in situ stress in deep coal beds, and for the efficient development of coalbed methane and the practice of geoengineering integration.