Projects involving junctions of light and dark tunnel in mountainous areas are complex engineering problems that combine tunnel structure, slope rock-soil mass and protection projects. Such junctions suffer from a complex and changeable load. The stress and deformation of the junction varies under different conditions. Thus, it is a major source of inconvenience for construction and monitoring operations. In this paper, according to the load conditions at a junction of light and dark tunnel, we divide the junction hole into thrust, compression, and combined thrust-compression types. Three types of structures were simulated by numerical analysis, and we explored the structural deformation and stress of these types of tunnel under different condition. Thus, in any construction process, the mechanical deformation mechanism and the weak point in the structure should be worked out. Based on the weak parts, some monitoring points were installed, and four fields for monitoring were chosen. The monitoring results show that the actual deformation, stress and structural failure location are basically consistent with the numerical simulation results. The deformation mechanism of light and dark tunnel junction obtained can provide the basis for selecting the treatment measures and controlling the structural deformation. Furthermore, the results can also be used as a reference for similar engineering design, construction and site monitoring projects.