In the context of new power systems, the increasing complexity of transmission grid structures poses new challenges for bundled delivery of clean energy sources across network sections. To address this issue, a heterogeneous energy complementary dispatching method is proposed that accounts for the smooth delivery across the transmission sections of the system. First, a mid- to long-term multi-objective optimal dispatch model is constructed with the objectives of maximizing power generation, minimizing transmission fluctuations across sections, and minimizing power curtailment. The model is solved by the NSGA-II algorithm. Then, to overcome the weak adjustment ability of the traditional NSGA-II algorithm in handling operational constraint violations when solving scheduling models dominated by cascade hydropower stations, a differentiated exploration matrix is introduced to optimize the mutation process, thereby enhancing the algorithm’s adaptive adjustment capability at constraint boundaries. Finally, taking the Yalong River clean energy base as an example, the applicability of the constructed three-objective model in describing the cross-section transmission problem of heterogeneous energy systems is verified by comparing the computational results across different typical years. Furthermore, the stronger adaptive ability of the improved NSGA-II algorithm is demonstrated by comparing the error rate and percentage of Pareto solution metrics before and after the improvement.