A case study is presented to identify the influence of continuous rainfall on surrounding rock-initial support system of shallow decomposed-rock tunnel. From March 21 to April 29, 2006, rainfall with intensities ranging from 25 mm/day fell several hours every day, resulting in the collapse of the tunnel crown after the initial support of the surrounding rock in a part of shallow tunneling bench sections of Xiang-an Subsea Tunnel, located in Xiamen, Fujian, China. The applied calculation method of 3D elastic–plastic numerical back analysis based upon FLAC3D is presented. Through site investigation, test and in situ monitoring, the surrounding rock physical-mechanics parameters and support parameters were obtained by the calculation of elastic–plastic back-analysis method presented here. Furthermore, the influence of continuous rainfall on the stability of shallow decomposed-rock tunnel was investigated using the proposed method. The results show that: (1) rainwater infiltration makes the surrounding rock of the shallow decomposed-rock tunnel continuously softened due to the continuous rain, resulting in decreasing surrounding rock stiffness and coefficient of confinement pressure; (2) the negative influence of groundwater must be considered on the initial setting and initial strength of shotcreting of shallow decomposed-rock tunnel under the action of continuous rainfall, to ensure the stabilization of surrounding rock-initial support system; and (3) tunnel stability analysis by the back-analysis method proposed in this study is reasonable and reliable, which could be used as a reference for the estimation of stability of the same type of tunnels and their design.