Initial condition of water surface elevation with boundary condition is required to simulate two-dimensional finite element model. In general, in order to perform two-dimensional finite element model, unrealistic initial water surface elevation which is above all-terrain bed elevation and unmatched downstream boundary condition is used, which will make it difficult to perform stably. In this study, the water surface elevation caused by the actual river bed rather than a fixed value is applied automatically as the initial condition of a two-dimensional finite element model. The algorithm to automatically extract river cross section for simulation of one-dimensional hydraulic analysis from a two-dimensional element mesh is developed. And the accuracy of twodimensional model tried to upgrade by improving the two-dimensional finite element model, which used the results of one-dimensional non-uniform analysis as the initial condition of two-dimensional model. To examine the applicability of an improved model, the model was applied to the rectangular channel with a rapid slope, mild-steep slopes channel, steep-mild slopes channel and Han River. The results of the model, which the initial water surface elevation of one-dimensional flow analysis is used, were more stably converged than those of existing model and the stability of numerical computation was improved by using physical initial water surface elevation.