To ensure the safety operation of inter-basin water transfer project, it is important to understand the seismic performance of shallow-buried large-scale segment-connected pipeline structure under earthquake and other multiple actions. In this paper, a 3D FE model is built in details for the seismic assessment of large-scale prestressed concrete inverted-siphon shallow-buried under riverbed, and a method is proposed to realize multiple interactions of the viscoelastic boundary elements to finite elements, the compressible fluid to structure and the sealed joints made of rubber belt between adjacent segments. The inverted-siphon is longitudinally composited by 58 segments in total length of 858.64 m, and transversally consisits of three rectanguler-section boxes with net dimension of each box of 6.5 m width and 6.6 m height. The main influencing factors are set as the thickness of overburden soil, the flow condition and the engineering geological condition. The time-history analysis is carried out on the 3D FE model under Elcentro seismic wave excitation. The numerical analyses figures out the main vibration modes and vibrational frequency of this inverted-siphon, reveals the regions of peak tensile stress appeared on the concrete surface and the risk sealed joints with extremum relative displacement. This provides a scientific reference to take specific prevention measures of anti-earthquake, based on a deep understanding to the seismic cracking of concrete and the tearing broken of sealed joints for this kind of segment-connected pipeline structure.