Operating rules have been widely used to handle the inflows uncertainty for reservoir long-term operations. Such rules are often expressed in implicit formulations not easily used by other operators and/or reservoirs directly. This study presented genetic programming (GP) to derive the explicit nonlinear formulation of operating rules for multi-reservoir systems. Steps in the proposed method include: (1) determining the optimal operation trajectory of the multi-reservoir system using the dynamic programming to solve a deterministic long-term operation model, (2) selecting the input variables of operating rules using GP based on the optimal operation trajectory, (3) identifying the formulation of operating rules using GP again to fit the optimal operation trajectory, (4) refining the key parameters of operating rules using the parameterization-simulation-optimization method. The method was applied to multi-reservoir system in China that includes the Three Gorges cascade hydropower reservoirs (Three Gorges and Gezhouba reservoirs) and the Qing River cascade hydropower reservoirs (Shuibuya, Geheyan and Gaobazhou reservoirs). The inflow and storage energy terms were selected as input variables for total output of the aggregated reservoir and for decomposition. It was shown that power energy term could more effectively reflect the operating rules than water quantity for the hydropower systems; the derived operating rules were easier to implement for practical use and more efficient and reliable than the conventional operating rule curves and artificial neural network (ANN) rules, increasing both average annual hydropower generation and generation assurance rate, indicating that the proposed GP formulation had potential for improving the operating rules of multi-reservoir system.