Abstract: Small hydropower-containing microgrids are susceptible to large power fluctuations caused by source-load uncertainty, and off-grid conditions can easily lead to power outages and power abandonment of the microgrid system. To fully consider the power and energy balance characteristics of microgrids containing small hydropower sources and improve their economy and robustness, this study proposes a method for optimizing the configuration of energy storage in microgrids containing small hydropower using the power and energy characteristics. First, the power-energy balance mechanism of a microgrid containing small hydropower is analyzed, and a power-energy characteristic model of the microgrid is proposed based on the power-energy characteristic model of the microgrid containing small hydropower and the source-load uncertainty model. A stochastic scenario decomposition clustering method based on the power-energy characteristic and the energy storage capacity configuration method is also proposed. Finally, the effectiveness of the proposed method is verified by comparing the results with those of existing methods and analyzing the influencing factors using an off-grid microgrid containing small hydropower in a region as a simulation example.