The Dongping No.1 Tunnel of the Guangdong–Foshan Loop Line Intercity Railway in China passes an existing large-scale underground pipe gallery in water-rich sandy strata through the undercutting method. During construction, controlling the underground pipe gallery deformation is difficult because the water-rich sandy strata can easily become unstable. To deal with this problem, this paper proposes a double layer pre-support system (DLPS) consisting of pipe shed and horizontal jet grouting piles, whose function mechanism is explored from the viewpoint of passive protection and active reinforcement. The deformation transferring path of the DLPS is described as follows: tunnel excavation → lower pre-support deformation → deformation of the soil between the upper and the lower pre-supports → upper pre-support deformation → underground pipe gallery deformation. Considering the influence of geological conditions, the proposed DLPS has two failure modes, namely, excessive settlement of the tunnel vault and excessive deformation of the overlying underground pipe gallery. The mechanical model and analytical method of the DLPS were established according to the theory of beam resting on elastic foundation. Comparing the computed and measured settlement values revealed that the established model is reliable because it could reflect the interaction characteristics of the upper pre-support, the lower pre-support, and the middle soil. Finally, multiple factor analysis was conducted to ascertain the influence of typical calculating parameters, and the deformation characteristics of the DLPS under different influence factors were obtained. The design suggestions for key parameters could provide reference for similar practical engineering in the future.