Abstract: As an important underground structure in water transfer projects, the inverted siphon structure is easily affected by earthquake and geological conditions, and the inverted siphon structure with shallow buried depth is more likely to affect the structural stability due to soil vibration. In this paper, the inverted siphon structure of a project will be selected as the research object, and the three-dimensional finite element dynamic response analysis will be carried out by using Newmark Time History Analysis Method to study the seismic response law of the inverted siphon under the geological type of medium soft soil. The results show that the peak acceleration response is about 1.4 times more than the maximum input acceleration, but it changes little along the height of the inverted siphon section. The x-direction displacement of each characteristic point of the horizontal section is greater than that of the inlet transition section. Staggered damage is apt to occur at the interface between the two pipe sections, and the maximum settlement is 13.6 mm, which is within the safety range. Under the Ⅶ degree earthquake, the maximum third principal stress is 3.23 MPa, which is less than the standard value of compressive strength of C20 concrete. The maximum first principal stress of inverted siphon structure is 1.48 MPa, which is equivalent to the tensile strength value and is prone to damage. The integral structure of inverted siphon under Ⅶ degree earthquake is in a safe state.