This study investigates the spatiotemporal evolution patterns and mechanisms of rock mass stability in deep three-dimensional intersecting tunnels, laying the foundation for precise control of rock mass stability in such structures. Based on finite element analysis, the stress field, plastic zones, and deformation evolution patterns of the rock mass at horizontal intersections and gradient change points were analyzed under different intersecting angles. Results indicate that as the inclination angle increases: Maximum shear stress in the roof at the horizontal junction increases by 5.44%, while that in the floor decreases by 5.75%; Maximum shear stress in the roof at the gradient change point increases by 17.52%, while that in the floor decreases by 10.90%. Stress concentration in the roof significantly intensifies and migrates toward structurally weak zones, while stress in the floor gradually transfers deeper into the surrounding rock. The thickness of the rock mass shear stress“shell”increased with the main stress difference, while the extent of the plastic zone and displacement showed a positive correlation with shear stress variations. Changes in inclination at the intersection caused differing stress field distributions, plastic zone sizes, and deformation increments between the roof and floor, thereby increasing localized rock mass instability risks in the roadway. Consequently, precise coordinated control of both roof and floor rock mass regions is essential during roadway support at intersections.