Food and energy security are important issues that threaten human survival and development. The rice-wheat rotation system provides a stable source of food for more than 20% of the world's population, but there have been no reports on the energy balance of different rice-wheat rotation systems. This study evaluates the energy inputs and outputs of three rice-wheat rotation systems and their energy production efficiency through the study of dry direct-seeded, wet direct-seeded, and transplanted rice-wheat rotation systems. The results of the study showed that the average total energy inputs in the dry direct-seeded, wet direct-seeded, and transplanted rice-wheat rotation systems were 58,677, 74,083, and 69,022 MJ ha(-1), respectively. The production resources with more energy input in rice-wheat rotation system were all related to water and fertilizer. The energy input in the rice season accounts for more than 50.69% of the total energy input in the rice-wheat rotation system. At the same time, rice-wheat rotation production is highly dependent on nonrenewable energy. Among the three rice-wheat rotation systems, the transplanted rice-wheat rotation system had the highest total energy output and net energy, while the dry direct-seeded rice-wheat rotation had the highest energy use efficiency, energy productivity, energy profitability, and human energy profitability. The results showed that the key to reducing the energy input in the rice-wheat rotation system is to reduce the amount of water and fertilizer. The transplanted rice-wheat rotation system is more suitable for promotion in rice-wheat rotation production areas with good irrigation conditions, while the dry direct-seeded rice-wheat rotation system is highly compatible with the current development direction of low energy consumption and high energy efficiency in agricultural production and is suitable for promotion in rice-wheat production areas with poor irrigation conditions.