Subway tunneling construction in shallow buried karst region is a common challenge. Survey boreholes and cross-hole seismic CT data showed that 29 karst caves exist at elevation of −17 m to −37 m in Si–He section of the Wuxi Metro Line 4, which are consisted of 18 filled caves and 11 empty caves and constitute substantial dangers to the stability and quality of metro construction projects. Based on their size, position, and type of filling, we divided these shallow karst caves into four types. Aimed at exploring the instability of the tunnel after excavation, numerical analyses have been developed by using the Finite difference method. Both the effects of the distance between tunnel and karst caves and the effects of the filling of the cavities on the overall stability of the rock mass around the tunnel have been investigated. According to the design criteria, safety distance between tunnel and karst caves was determined. The monitoring data of tunnel during excavation proved the rationality and accuracy of the analysis results. The research results can provide technical reference for the design and construction of other proposed tunnels that are located in the regions of shallow buried karst in Jiangsu Province.