Although compressibility is a critical aspect of groundwater, research on this factor has been primarily limited to laboratory tests and theoretical analyses. Thus, the effects of this property on engineering applications, such as deep excavations, are unclear. In this study, a numerical model combined with the hydro-mechanical coupled method is established to analyze the impact of the compressibility of gassy groundwater (CGG) on the performance of deep excavations in Shanghai deposits, which are characterized by a typical composition of multi-aquifer–aquitard. A reasonable agreement between the numerical results and the measured data of three projects of deep excavations is achieved, verifying the established model's applicability. The results suggest that the deformation behavior of excavations increases significantly with the increase in CGGs. The impact of CGGs on excavation deformations can be attributed to the variation of the stress level inside the excavation and the pore water pressure outside the excavation. Furthermore, an equivalent CGG in the analyses of deep excavation involving dewatering-only in Shanghai soft deposits is suggested as a high value ranging from 1 × 10−7 m2/kN to 1 × 10−6 m2/kN, providing an available reference for the analyses of deep excavations in Shanghai while considering the effect of CGGs.