To reveal the large deformation mechanism of surrounding rock in Grade Ⅵ water-rich soft rock tunnels and verify the supporting effect of comprehensive deformation control measures dominated by double-layer primary support, a case study is conducted on the Shanyang Tunnel of the Dali-Ruili Railway, and a viscoelastic-plastic analytical solution for Grade Ⅵ water-rich soft rock tunnels with double-layer primary support is established based on the post-peak stiffness and strength deterioration model of soft rock. Verified by field monitoring data and numerical simulation results, relevant influencing factors of surrounding rock deformation are systematically analyzed. The main conclusions are drawn as follows: (1) For high insitu stress Grade Ⅵ water-rich soft rock tunnels, the surrounding rock is dominated by compressive deformation in the early stage and loosening deformation in the later stage after excavation. The surrounding rock deformation is greatly affected by weak lithology, groundwater softening effect, and insufficient structural resistance of primary support. (2) The comprehensive control measures integrating double-layer primary support, optimized excavation section, and shallow surrounding rock grouting can effectively restrain the large deformation of such soft rock tunnels, limiting the surrounding rock deformation within 20 cm. (3) The double-layer primary support perfectly conforms to the support principle of “yielding pressure first and then strengthening support”. The total displacement of surrounding rock decreases with the increase of support resistance, and the support resistance exerts a far more significant influence on the late creep deformation than the early instantaneous deformation of surrounding rock. (4) In the construction process of double-layer primary support for high insitu stress soft rock caverns, the outer primary support suffers a larger total deformation due to the early installation time. The development of yielding-type double-layer primary support is recommended for follow-up related researches.