Identifying an energy-efficient system with low energy use, low global warming potential (GWP), and high profitability is essential for ensuring the sustainability of the agro-environment. Given the global importance of China’s rice production, this study determines energy, environmental, and economic performances of transplanted (TPR) and direct-seeded rice system (DSR) in central China. The results showed that total energy inputs for TPR and DSR were 31.5 and 22.8 GJ ha− 1 across two growing seasons, respectively. Higher energy input for TPR primarily resulted from extra energy use of the nursery beds and transplanting. Higher energy output of DSR (202.5 GJ ha− 1) over that of TPR (187.7 GJ ha− 1) was due to a slightly higher yield from DSR. Therefore, DSR exhibited significantly higher energy use efficiency than that of TPR. Lower specific energy for DSR (2.78 MJ kg− 1) relative to TPR (4.02 MJ kg− 1) indicated that the energy used to produce per unit of rice grain could be reduced by 30.8% by adopting DSR. On average, GWP of DSR was reduced by 5.6% compared with TPR. Moreover, DSR had a 55.8% higher gross return and a 25.7% lower production cost than those of TPR. Overall, compared with TPR, DSR has the potential to increase gross economic return and energy output with reduced energy input and emissions. Therefore, this study suggests that DSR is an environmentally-sound and economically-viable production system. As such, DSR is noted as an energy-efficient and climate-smart production system that could be used by policymakers and farmers to achieve not only improvements in the environment but also financial benefits.