Abstract: In weak-grid regions the backbone network is fragile and outward transmission corridors are constrained, so that local consumption of clean energy and reliable power supply mutually constrain each other. Starting from energy conservation, the thermodynamic reversibility of water electrolysis and multi-time-scale power balance, hydropower is employed as the continuous regulating source and green hydrogen as the long-duration energy carrier. A four-level coordinated system is thereby constructed that covers the second-to-minute scale (hydropower governor and battery energy storage), the daily scale (daily-regulating hydrogen) and the weekly-to-seasonal scale (seasonal hydrogen and reservoir). Seasonal-trend decomposition (STL) and variational mode decomposition (VMD) are used to extract the spectral structure of source–load imbalance power; once the charge/discharge states of hydrogen storage are fixed a priori, the scale of the mixed-integer program is reduced. A bi-level capacity-configuration model that minimises life-cycle comprehensive cost is established: the outer layer searches equipment sizes, while the inner layer verifies the annual operating trajectory and continuous 168-hour off-grid autonomy. The self-balancing rate is required to be no lower than 0.8. Under identical hydrological, meteorological, load and hydro–wind–solar installation sequences, three schemes are compared: a three-level electricity–hydrogen structure (hydropower used only as an energy source), a four-level structure without feature extraction, and a four-level structure with predetermined hydrogen actions. After the low-frequency regulation channel of hydropower is opened, seasonal hydrogen storage capacity falls from 420 MW·h to 280 MW·h, the self-balancing rate reaches 0.88, relative comprehensive cost is reduced by 22% compared with the three-level structure, and relative solution time drops to 35%. Within the 168-hour extreme low-output window, reservoir storage, battery state-of-charge and both levels of hydrogen inventory remain within limits. A verifiable theoretical pathway and configuration method for independent networking of weak grids are thereby provided.