Traditionally, in the pursuit of economic development, ecological health was sacrificed, but this is no longer tenable considering the vast environmental damage that is difficult to control and expensive to repair. This is especially true for China’s Jianghuai River Basin (JRB). As a result, this paper uses the slacks-based measure (SBM) directional distance function and the tobit model on panel data from various cities and counties in the Jiangsu section of the HRB to empirically analyze regional green agricultural production efficiency and influencing factors from 2005 to 2019. The results illustrate that agricultural and environmental efficiency fluctuate upward in provincial areas. Still, a downward trend is observed in both redundancy and insufficiency rates of undesirable and desirable output. While this indicates improving regional agricultural and environmental efficiency, there is no readily detectable positive effect of technological progress and technical efficiency on green agricultural production efficiency improvements. Following a full analysis, policy implications are presented and discussed.