This paper proposes a new storage allocation rule based on target storage curves. Joint operating rules are also proposed to solve the operation problems of a multi-reservoir system with joint demands and water transfer-supply projects. The joint operating rules include a water diversion rule to determine the amount of diverted water in a period, a hedging rule based on an aggregated reservoir to determine the total release from the system, and a storage allocation rule to specify the release from each reservoir. A simulation-optimization model was established to optimize the key points of the water diversion curves, the hedging rule curves, and the target storage curves using the improved particle swarm optimization (IPSO) algorithm. The multi-reservoir water supply system located in Liaoning Province, China, including a water transfer-supply project, was employed as a case study to verify the effectiveness of the proposed join operating rules and target storage curves. The results indicate that the proposed operating rules are suitable for the complex system. The storage allocation rule based on target storage curves shows an improved performance with regard to system storage distribution.