This paper is based on the first stage of a water channel project of the Haiyang nuclear power project in Shandong Province. Using a dynamic time history response analysis method, we establish a three-dimensional soil structure model using the nonlinear finite difference software FLAC3D. We analyze the internal force changes of the nuclear power station's water channel under the combined effect of weight, water pressure, soil pressure, temperature, water hammer pressure, and seismic load. We carried out the seismic analysis of the inlet and outlet of the nuclear power station by FLACE3D programming, and calculated the internal force of the lining structure using a five-point formula. First, we addressed the internal force changes of the inlet-outlet channel position under the combined effect of weight, water pressure, soil pressure, temperature, water hammer pressure, and seismic load. Secondly, we selected three typical conditions and performed a comparative analysis of the internal force of the inlet-outlet position with different wall thicknesses. The calculation results show that: (1) Temperature has a significant effect on the internal channel outlet position if the internal temperature is greater than the external temperature. (2) Water hammer pressure force has a significant effect on the outlet of the channel, which can be used as a control condition for static analysis. (3) Seismic load also has a significant effect on the outlet of the channel, which can be used as a control condition for seismic analysis. (4) Different wall thicknesses also have a significant effect on the outlet of the channel; the thicker the wall thickness, the greater is the internal force. Therefore, based on the above conclusions, weak cross sections should be reinforced when being designed and constructed. The calculation method and analysis results in this paper can provide a reference for seismic response analysis of water channels in the nuclear power plants and in other similar structures.