Intensive cropping systems with two or three harvests per year are vital to produce sufficient food for the growing population. Improvements in the sustainability of these systems are critical for global food security. Transplanted double-season rice (TPD), an important cropping system in China, is seriously threatened by various challenges such as labor shortage, poor resource use efficiency, high environmental footprint, and low profitability. These challenges could be potentially alleviated by shifting TPD to direct-seeded double-season rice (DSD). Due to the limited thermal energy, ultrashort-duration cultivars matured within 95 days have to be used in DSD in central China. However, it is unknown whether DSD with ultrashort-duration cultivars (DSDS) can improve resource use efficiency and reduce environmental costs compared with TPD in this region. This study aimed to compare the resource use efficiency (energy, water, labor, and fertilizer), carbon and nitrogen footprints, and net ecosystem economic benefit of DSDS and TPD with ultrashort-duration (TPDS) and medium-duration cultivars (TPDM). Results showed that total energy output was 222.0 GJ ha−1 in DSDS, which was comparable to that of TPDM but was significantly increased by 9.5% compared with TPDS. Compared with TPD (i.e. both TPDS and TPDM), the total energy input, labor input, water input, and nitrogen surplus in DSDS reduced by 16.9%, 53.2%, 36.8%, and 31.4%, respectively, leading to significant increases in energy use efficiency, labor productivity, water use efficiency, and nitrogen use efficiency. Furthermore, DSDS decreased direct CH4 and NH3 emissions and indirect carbon emission and reactive nitrogen losses from agronomic inputs, and consequently reduced carbon footprint by 28.6–42.7% and nitrogen footprint by 12.9–14.8% compared with TPD. As a result, the net ecosystem economic benefit in DSDS was significantly increased by 65.9–188.2% relative to TPD. These findings suggest that DSDS is a highly promising strategy to maintain high productivity with less resource inputs and environmental pressures but high economic benefits in central China.