A multi-function weir is representative control structure in the stream flow. Estimation of accurate flood discharge according to gate operations and prediction of floodwave travel times at the downstream are very important in terms of water use and river management. This study analyzed the limitation and improvement through the current gate operation data on the Young-san river. in addition, flood discharge was calculated considering lower and upper water level condition and gate operating using the modified slope-area method in the Seoung-chon weir. As a result, the current state was required improvement because exceed the theoretical range and rapidly fluctuation of discharge coefficient, can not be considered difference between the upper and lower water level and the estimation by the regression equation. As a result of applying the proposed method in this study, the above mentioned limitations can be compensated, compared with the current discharge data. Also it was analyzed as more physically valid because using the evaluated hydraulic equation and estimate the slope and friction loss of natural stream by iteration and to reduce the error. In conclusion, the process carried out serves as a representative flow control point of the water system through reliable discharge estimation, it is expected that it will be possible to properly river management.