This study investigates the disturbance of bridge piles caused by the adjacent deep excavation of a metro station in Guangzhou while considering the existence of underlying karst caverns. Ground treatment was adopted to reduce the effects of the deep excavation on the surrounding environment, including metro jet system (MJS) technology and karst treatment. Considering the presence of karst cavern and an inhomogeneous limestone layer, three-dimensional nonlinear finite element analysis (FEA) was implemented to investigate the excavation-induced effects on the surrounding ground and structures. Coupled pore fluid diffusion and stress analysis were adopted for the excavation simulation, and comparative analyses between the field data and FEA results were used to verify the numerical model. A series of parametric studies were conducted by varying the parameters of the MJS piles and karst cavern filling. This study reveals that: (1) increasing the Young’s modulus of the MJS pile leads to a decrease in ground and wall settlement; (2) the optimal buried depth of MJS piles is the depth that reaches the rock stratum; (3) the optimal MJS pile–wall distance is 0.225H (H denotes excavation depth); (4) increasing the piles diameter leads to a linearly decrease in wall and piles settlement; and (5) varying the Young’s modulus and permeability coefficient of the karst cavern filling has little effect on the surrounding environment. MJS treatment can be used as an effective measure for protecting the surrounding environment from disturbance by deep excavations.