In recent years, there has been a new top overflow hydropower plant which arranges discharge way and electricity generation flow way to overlap, and it is an important problem that whether flow fluctuation will affect the structural safety in the operation process. In this article, flow fluctuating of a new top overflow powerhouse was simulated by means of large eddy simulation. Combined with the relevant test results, we obtained the distribution characteristics of flow fluctuating of the hydropower house. The results show that flow fluctuation frequency is far different from the natural frequency and does not cause structural resonance, so the structure is safe.