To ensure the construction and operational safety of tunnel undercrossing multi-situational goafs, the Huaying Mountain High-Speed Rail Tunnel, a critical section of the Xi’an-Chongqing High-Speed Railway, was taken as a case study. Based on a three-dimensional finite difference numerical simulation platform, twelve situations were established to analyze the effects of three factors: distance, scale, and angle. The stability analysis was conducted by examining the displacement and deformation characteristics of the surrounding rock, stress changes, and axial forces of the initial support for each situation. The results show that in tunnel undercrossing multi-situational goafs, the vertical deformation, horizontal convergence of the surrounding rock, and the maximum axial force of initial support are all affected. Within a certain range, changes in distance significantly impact subsidence and settlement deformation of the surrounding rock. However, as the distance increases, the horizontal and vertical displacements of the tunnel and the axial force of the initial support tend to decrease. Conversely, the scale and angle of the goaf have an opposite effect on the surrounding rock: as the scale and angle increase, the stability of the surrounding rock deteriorates. In this case study, when the distance exceeds 1.13 times the tunnel span, the influence of the goaf on the stability of the surrounding rock gradually decreases. When the angle exceeds 45°, vertical displacement decreases, and the increasing trend of horizontal displacement gradually diminishes. The conclusions of this paper can provide guidance for designing reinforcement schemes for tunnels crossing through multi-situational goafs. The findings provide valuable insights and guidance for similar engineering projects.