The deformation characteristics and the timing for secondary lining support in high geo-stress soft rock tunnels have drawn significant attention. In carbonaceous shale formations, tunnel construction deformations are very pronounced under construction disturbances due to the development of joints, dense fractures, and poor interlayer bonding. With the Xishuangbanna tunnel as our research backdrop, this study meticulously analyzed the deformation patterns and characteristics inherent to high geo-stress tunnels constructed within carbonaceous schist formations. Employing a comprehensive approach involving full displacement analysis and on-site construction mechanics testing, we utilized the displacement release rate and structural safety factors as key indicators to determine the secondary lining supporting time. Employing this innovative approach, we successfully identified the ideal junctures for implementing secondary lining support in tunnels excavated through high geo-stress carbonaceous schist. The research findings indicate that the primary damage modes in high geo-stress carbonaceous schist tunnels are initial support failure and extensive early support deformation. These vulnerabilities are primarily attributed to weak and fragmented strata, elevated ground stress levels, and inadequate support strength. During the early stages of tunnel construction, substantial deformations are observed, exhibiting high rates of change. Horizontal convergence, notably, significantly surpasses the settlement at the tunnel’s crown. When employing the three-bench method for construction, the deformation occurring before the excavation of the middle bench contributes the most to the total deformation monitored, whereas the deformation generated after the excavation of the inverted arch constitutes a minor proportion. The tunnel’s crown and invert experience tension while the secondary lining undergoes compression. The internal forces are most significant at the tunnel’s hance and knee, with the left tunnel knee being the weakest section of the secondary lining. The findings of our study are poised to guide the design and execution of tunnels constructed within high geo-stress carbonaceous schist formations.