Based on viscous damping system dynamics equation, seismic dynamics equations of fluid-solid interaction problems with stress-related complex damping theory are established. Fluid-solid interacion 3D fem dynamic program for solving Rayleigh damping model and complex damping model structure is developed with newmark-b integration method. The seismic time history response and loss factor of a deepwater thin-walled steel pipe pier are calculated.Two kinds of response of considering fluid solid interaction effect and without regard to fluid solid effect are studied.It shows that the response with complex theory is bigger than that of Rayleigh damping theory far under El-Centro earthquake load with peak value 2m/s2. The seismic response with consideration for fluid solid interaction is half as much again to twice bigger than that without consideration for fluid solid interaction.The loss factor increases with the stress or response and the loss factor with consideration for fluid solid interation is obviously bigger than that without regard to fluid solid interaction.