Abstract: High precision numerical simulation of one-dimensional complex flow in natural rivers is still faced with great difficulties under the condition of rapid change of cross-section geometry. Based on the Godunov Scheme,a flux calculation method for HLLC approximate Riemann Solver based on the conservation type Saint Venant Equation is proposed. The solver is extended from the shallow water equation to the conservative Saint Venant Equation. A variable space reconstruction method for natural rivers with complex cross-section geometry is proposed. According to the equivalent principle of flow section area and static moment,the cross-section is generalized into a rectangle. The cross-section geometry at the interface of the element is constructed by linear interpolation. According to the reconstruction results of water level,the reconstruction values of flow section area and static moment on both sides of the interface are calculated. The conservation of calculation format is guaranteed. The case study shows that under the condition of rapid change of cross-section geometry of natural rivers,the calculation results of the proposed method are in good agreement with the measured values,and it has high simulation accuracy for mixed flow.The research results provide a new method for the high precision numerical simulation of natural river hydrodynamics and environmental hydraulics.