There are several large karst caves at haunch part of the Lidong Tunnel during construction, together with inrush water due to high pressure within these caves. In light of it, this paper takes YK342+113 section as an example and adopts finite difference software FLAC 3D, so as to analyze tunnel deformation when crossing karst caves under six different working conditions, including with or without karst cave, before and after karst treatment, along with support locations. According to analysis results: (1) the wall rock mainly had deformation at tunnel vault when evacuating at the third bench, which is a critical monitoring focus for tunnel construction; (2) karst cave treatment contributed to better conduct forces on both sides of wall rock, thus reducing vault settlement, while not affecting horizontal convergence and upturn of vaults; (3) treatment measures were proved to be effective in minimizing wall rock deformation by comparing deformation curves under different conditions; (4) after treatment measures, the angular points within the cave’s chamber had stress concentration, which might cause secondary collapse. Field monitoring data revealed that the final settlement of the tunnel vault was relatively consistent with the numerical analysis results, with a distinct change in daily settlement after initial support construction. By integrating numerical analysis and field monitoring, the rationality of the karst treatment plan was fully verified, providing a valuable reference for similar projects.