Interconnections of rivers and lakes, which can improve short-term water qualities in lakes, have been widely used in China. It is necessary to search for the reasonable discharge of pollution flushing in order to achieve the best flushing effect as well as the lowest cost. In this paper, the water environmental improvement effect of different flushing discharges is analyzed, using the two-dimensional water quality mathematical model based on DEM. Furthermore, the cost and benefit evaluation method is put forward to find the quantitative relation between pollution flushing discharges and project benefits. Based upon the Lake Cihu project, the pollution flushing discharges and project benefits curve has been obtained by simulating eight different flushing conditions. The results indicate that with the increase of pollution flushing discharge, the benefit first increases and then decreases, while the maximum benefit is about ￥40500, and corresponds to an optimal pollution flushing discharge of 10.62 m³/s. This study could provide scientific basis for pollution control and cost control in Lake Cihu and other similar lakes with the river-lake interconnection systems.