In order to study the influence of different reservoir water models on arch dam structural dynamic characteristics, an added masses model and fluid solid interaction(FSI) system model of a Laxiwa arch dam were set up. The results of finite element simulation were compared with the identification results of stochastic subspace identification (SSI) based on wavelet threshold combined with the empirical mode decomposition (EMD) filtering method. The comparison shows that the structural dynamic characteristics were reflected by both coupled models, and the frequency error margin for the added masses model calculation results to the identification results was 0.41%~7.55%, while that of the FSI system coupled model was 0.09%~3.19%. The FSI system model was superior to the added massed model with a smaller error at each frequency order. Additionally, the frequency space of contiguous order of the FSI system model was relatively stable. This study shows that the FSI system coupled model can reflect the arch dam vibration information comprehensively and accurately in terms of simulation order number and precision. The FSI system coupled model can be applied in the dynamic characteristics analysis of arch dam structure, and used as a reference of the finite element model in the research of diagnosing arch structural damage.