Ratoon rice (RR) system is an alternative to the double-season rice (DR) system in central China due to its high annual yield and relatively lower cost and labor requirement. However, the effect of conversion from DR to RR on the carbon footprint (CF) and net ecosystem economic benefit (NEEB) remains largely unknown. Here, we elucidated the effect by using two early-season rice varieties (ZJZ17, LY287) and two late-season rice varieties (WY103, TY390) for the DR system, and two RR varieties (YLY911, LY6326) for the RR system. The six varieties constituted four cropping systems, including DR1 (ZJZ17 + WY103), DR2 (LY287 + TY390), RR1 (YLY911) and RR2 (LY6326). The two-year experiment demonstrated that RR had 27.37% lower annual CF than DR, which could be attributed to the significantly lower annual CF (by 87.27%) of ratoon crop in RR relative to that of the late-season rice in DR. Direct greenhouse gas (GHG) emissions contributed the most to annual CF in both systems, accounting for 43.28% and 35.39% in DR and RR, respectively. Furthermore, conversion from DR to RR system significantly increased annual NEEB by 30.95%. This increase could be attributed to the 20.25% higher annual grain yield of main crop in RR relative to early-season rice in DR, and 75.32% and 87.27% lower annual costs for agricultural inputs and CF of ratoon crop than late-season rice in DR, respectively. Rice variety also showed certain effects on the yields and GHG emissions in different RR systems. Compared with RR1, RR2 significantly increased annual yield and annual NEEB, while decreased annual CF and annual yield-scaled CF (CF_y). These findings suggest that the conversion of the DR system to LY6326 RR system may be a highly promising strategy to simultaneously reduce CF, promote NEEB and maintain high grain yield in central China.