For the complex inter-basin joint operation of water transfer from two water delivering areas to the same water receiving area, an multi-objective model of joint optimal operation was established, with which an optimal operation rule formulation process was constructed based on the theory and method of large system decomposition and coordination (LSSDC). And then, this model was applied to the water transfer projects of Hanjiang to Weihe River and Jialingjiang to Hanjiang River which are located in Hanjiang River Basin and Jialingjing River Basin of Shannxi Province respectively. With the long time series analysis of 55 years, the internal compensation of the complex water transfer system and its capability of joint optimal operation were verified. The results show that the large complex system can effectively improve the efficiency of water transfer, greatly reduce the fluctuation of water transfer process, so it is more conducive to the actual operation of the projects.