The graph theory model in transportation and the network analysis method in landscape ecology are introduced into the optimization of river basin connectivity. Two improved methods, the reticulate connectivity index(RCI)method and the comprehensive connectivity index(CCI)method, which are suitable for the quantification of comprehensive connectivity of reticulate river network with strong artificial disturbance, are proposed to optimize the connectivity of Qingyi River Basin. The results show that the two methods are consistent in the trend of quantification of the importance of a single gate or dam. After optimization, the CCI of Qingyi River Basin increased from 26.13 to 38.34, and the connectivity improves significantly. The improved RCI and CCI can be used to quantify and restore the connectivity of the reticulate river network.