Regional integrated energy systems (RIES) represented by hydro, wind, and solar energy are crucial avenues for future clean energy development, fully leveraging their complementarity can facilitate the orderly supply of renewable energy, significantly enhance the level of new energy consumption, and make outstanding contributions to achieving carbon neutrality goals. However, run-of-river hydropower (RHP), wind power (WP), and photovoltaic (PV) are affected by the chaotic characteristics of the weather system, with significant random fluctuations, and their output characteristics have significant heterogeneity, which brings a big challenge for the complementary coordinated scheduling. The high-accuracy power prediction of RHP, WP, and PV in the region is one of the key means for solving the above problems. To meet this challenge, by analyzing the spatio-temporal correlation properties between weather processes and station output, a novel joint prediction framework for short-term power forecasting (STPF) of regional hydro-wind-PV clusters is proposed. Firstly, to solve the problem of significant heterogeneity of water, wind, and solar, a Differentiated Spatio-Temporal Mixture Network (DSTMN) is proposed, which differentially encodes the weather and power information at multiple locations, enabling the extraction of common features while preserving their specificities, which addresses the difficulty of representing the inherent correlation patterns between wide-area meteorological information and heterogeneous energy sources. Secondly, to further explore the spatio-temporal correlation between meteorological information and power information, to improve the forecasting performance of the model, a spatio-temporal-lagged correlation (STLC) that can quantify their spatio-temporal delays is proposed. By analyzing the correlation characteristics between regional grid numerical weather prediction (NWP) information and station output at different spatial and temporal scales, the optimal spatial location and delay time of NWP inputs under the current scenario are determined for each station. Based on this, the best NWP scene probabilistic transfer model is established based on the Rank Bayesian Ensemble (RBE) method. By fitting the conditional probability distribution of the current best NWP spatiotemporal location and the 2nd day’s best NWP spatiotemporal location, providing a reliable input for the STPF model. Finally, a case study with 164 hydro-wind-solar stations in China demonstrates the effectiveness of the proposed method. Specifically, we achieved an accuracy improvement of 0.46% — 11.03% on the 2nd day of forecasting compared to benchmark methods.