Background: As the two main forces of China’s power electricity, the energy generation efficiencies of thermal power and hydropower are important factors affecting the energy conservation, emissions reduction, and green development of the country’s whole power industry.Methods: Considering regional differences and multiple effective decision-making units, this research uses the Meta-SE-SBM undesirable model to comprehensively evaluate the efficiencies of hydropower and thermal power generation in China, taking CO2 emissions of thermal power generation as the undesirable output.Results: The average group efficiency of thermal power generation in the central region has greatly improved, the eastern and western regions also show an upward trend, but there is a slight downward trend for hydropower in the three regions. The hydropower technological gaps in the three regions have slightly expanded, but their thermal power technology gaps have gradually narrowed. From the perspective of input-output non-efficiency level, the undesirable output CO2 of thermal power energy efficiency in the eastern, central, and western regions is in a surplus, the redundancy of equipment utilization hours, energy input, and installed capacity in the western region are all high, but generation in the western region is insufficient, leading to relatively low efficiency of thermal power generation there. In the eastern region the redundancy of equipment utilization hours, number of employees, and installed capacity are all high, but the generation of hydropower in the eastern and central regions is insufficient, leading to relatively low hydropower efficiency in these two regions.Conclusions: When formulating policies to promote China’s power efficiency improvement and green development, the government and power industry managers should fully consider regional differences in the efficiencies of hydropower and thermal power. The thermal power industry is relatively mature, but its CO2 emissions should be reduced and the scale of thermal power cannot be blindly expanded. The hydropower industry needs further policy support to increase market share and to enhance the local power industry’s competitiveness under the condition of its resource endowments.