The submerged floating tunnel (SFT) is an innovative underwater traffic structure. The mechanical modeling and the structural response caused by traffic loads for this kind of underwater floating structure under complex boundary conditions deserve further study. In this paper, the SFT supported by multiple intermediate anchor cables is considered as an elastic supporting beam, and the complex boundary conditions at both ends are considered as vertical and rotational elastic supports with different constraint stiffness. The fluid load is considered by the Morison equation. The dynamic model of the SFT under arbitrary load is built, and the corresponding characteristic equation is established to consider the natural vibration characteristics. The frequencies and modes for multiple combinations of intermediate supporting stiffness and boundary constraint parameters are studied, and the corresponding sensitive intervals are obtained. At the same time, a high-speed train is taken as background and it is considered as a series of moving concentrated force. The relationship between the load response at the key position of the SFT structure and the stiffness of the elastic support is studied. The results show that the stiffness of the intermediate supports and boundary constraints all has significant effects on the vertical displacement. The larger the constraint stiffness is, the smaller the vertical displacement is.