An unsteady siphon flow model with two initial nature dynamic flows was established. The property of the unsteady siphon under different initial conditions was analyzed by applying Computational Fluid Dynamics (CFD). The siphon import cumulative momentum analysis results show that the dynamic initial flow conditions have an obvious impact on the property of unsteady siphon flow. Based on the results of CFD, an optimal solution of initial flow conditions was obtained by GA-ANN method. It provides a reference to the design of siphon runner and the research of unsteady siphon flow.