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.