A rapid coal phase-out is critical if China is to achieve carbon neutrality by 2060. However, this presents a significant challenge in maintaining system flexibility as the number of coal power stations reduce and renewable energy penetration increases. Here we analyze the interactions between flexibly operating hydroelectric facilities in balancing the decommissioning of a typical 600 MW coal-fired power unit across three different provinces with different electricity mixes. Rather than using a constant parameter for the carbon emission intensity for coal, as used in previous studies, we use dynamic intensities across different output levels. Accounting for the higher emission intensities of coal power plants running at below optimal efficiency to provide flexibility increases emissions from 3.4 % to 11.1 % depending on the region. The coal phase-out lowers flexibility indicators, with loss-of-load increasing in the full phase-out scenario in the absence of mitigating technologies such as electricity storage. Flexible hydropower eases peak demand issues significantly and the operating range of hydro-units has no significant effect on system flexibility or emissions. Overall, hydropower shows large potential in supporting decarbonization while maintaining system flexibility, especially for coal-dominated countries with abundant hydropower resources.