To support the construction of new power systems, the role of hydropower has gradually shifted from being solely an “power supplier” to an “power supplier + flexible regulator”. However, traditional day-ahead scheduling methods for hydropower do not account for short-term power balancing at intra-day or real-time scales, limiting their ability to cope with short-term new energy fluctuations. To address this issue, a multi-time scale scheduling method for cascade hydropower systems with hybrid pumped storage is proposed to fully explore the flexible regulation potential of hydropower. First, based on the operation characteristics of hybrid pumped storage, its new energy consumption capacity is analyzed, along with challenges in participating in real-time power balancing from both energy and water perspectives. Second, a multi-time scale scheduling framework for an integrated hydro-wind-thermal-storage system is constructed. In the real-time stage, the concept of an allowable fluctuation range of reservoir water level is introduced to limit the water level fluctuation between the end-of-period and target water levels, thereby ensuring compliance with medium- and long-term reservoir level boundary conditions. Finally, case studies are carried out on the IEEE39-bus system with the objective of minimizing total system cost. The results show that incorporating hybrid pumped storage into real-time power balancing improves the system regulation capability and facilitates safe, economical, and low-carbon operation.