Hydropower can be a renewable and alternative flexible option to support large-scale variable renewables integration, but the natural ‘battery’ role of cascade hydroplants remains unclear in decarbonization. Here, we present a multiscale assessment framework based on chance-constrained programming to quantify the changing role of hydropower in low-carbon energy systems. The framework includes optimal coordination expansion and base expansion models corresponding to the changing ‘battery’ and original power supplier, respectively. In addition to modeling operations of run-of-river hydropower, along with wind, solar, and coal and storage, the models, consider detailed hydraulic and electric coupling characteristics of cascade hydroplants and are transformed into mixed integer linear programming. Applying this approach to Yunnan clean energy system in Southwest China, we established that hydropower plays a crucial role in decarbonization by implementing comparative numerical experiments characterized by variable renewables penetration levels, hydrological years, and carbon emission levels, namely: 1) Compared with the current operation mode, the transformable hydropower could potentially decrease 14 GW storage investment and 6 GW of coal utilization by strategic hydropower operation. 2) Hydropower could reduce the triggering of other flexibility options by providing multiscale flexibility. 3) Decarbonization costs are expected to decrease by 36.6% on the path to zero carbon.