The southern rice region is a dominant area for double-cropping rice production in China, and the improvement of its green production efficiency has attracted widespread attention. Based on provincial panel data from 2003 to 2023, this study constructs an input-output indicator system that incorporates undesirable outputs. The DEA-SBM model is employed to measure the green total factor productivity (GTFP) of double-cropping rice in the region, and a multiple linear regression model is used to empirically analyze the influencing factors of GTFP, with robustness tests conducted. The results show that: (1) During the study period, the traditional total factor productivity (TFP) index was generally higher than the GTFP index. The annual average value of GTFP index was 1.010 4, indicating a gradual improvement in the GTFP of double-cropping rice in the southern rice region of China. (2) There were significant differences in the driving factors of GTFP growth among the ten provinces (autonomous regions) in the southern rice region of China. Specifically, GTFP growth in Zhejiang, Anhui, Fujian, and Hubei was driven by both green technological change (GTC) and green technical efficiency(GEC); Hunan, Guangxi, and Hainan relied mainly on GTC; while Guangdong, Jiangxi, and Yunnan were primarily driven by improvements in GEC. From the perspective of regional grain production and consumption characteristics, GTFP growth in major grain-producing areas followed a dual-driver pattern, major grain-consuming areas were driven by GTC, and grain-balanced areas depended on GEC. (3) Decomposition analysis of GTFP shows that under the “dual carbon” goals, the growth of GTFP in the southern rice region’s double-cropping rice sector was mainly attributed to GTC. (4) Agricultural economic development level, industrial structure index, and planting benefit level had significant positive effects on GTFP, whereas technological progress level and environmental regulation intensity exerted significant negative impacts.