The premise for the electricity market to effectively allocate resources is its ability to fully recognize resource value. However, existing valuation methods struggle to reflect the real multidimensional value of clean energy within the power system, resulting in a mismatch between market revenues and the actual value it contributes. To address this issue, this paper focuses on regulated hydropower units and proposes a decoupling modeling and quantitative evaluation method for multidimensional value of hydropower based on substitution benefits. First, the value of hydropower units in low carbon emissions, flexible regulation, and power supply is analyzed, along with its alignment with market revenues. Then, a decoupling and quantitative evaluation framework is proposed based on substitution benefits, representing hydropower units’ multidimensional value through system cost variations resulting from its integration. Comparative scenarios are designed to facilitate decoupling and quantification of hydropower units’ value. Subsequently, a time-series production simulation is conducted to capture market participants’ dynamic operational behavior and system cost changes under different scenarios, enabling the quantitative characterization of hydropower units’ multidimensional value. Case studies based on real power grid data illustrate that the multidimensional value of hydropower units is closely related to their operating conditions and system operation status, with significant variations across different scenarios. However, current market mechanisms fail to effectively reflect these value differences, providing insufficient incentives for high-performing hydropower resources. The relevant analysis results provide support for the improvement of market mechanisms.