With the sharply increased development of variable renewable energy resources (VRERs) in recent years, the hydro-wind-photovoltaic (PV) hybrid system (HWPHS) has the prospective to enhance the grid integration of VRERs. Nevertheless, the intense variation associated with wind and PV generation causes uncertainties in the long-term operation of the HWPHS. To overcome this drawback, this paper develops a novel method to derive adaptive operating rules for a cascade HWPHS. First, a scenario-generating method coupling Kernel density estimation with the copula function is proposed to characterize the wind and PV forecast errors. Second, based on the power generation scenarios, an optimal scheduling model for the cascade HWPHS considering transmission section constraints is proposed to simulate the hydro-wind-PV complementary operation; finally, the long-term operating rules for the cascade HWPHS are extracted by grey relational analysis and BP neural network. As a case study, the HWPHS of the Wu River basin in China is chosen. Results demonstrate that the proposed model can effectively utilize the flexibility of cascade hydropower stations, improve transmission section utilization efficiency, and promote clean energy absorption.