With the Chinese government promoting the “Double Carbon” policy and high-economic development, environmental regulation and economic efficiency research has become a hot topic. However, existing research focuses on industrial economic efficiency, ignoring logistics industry, which has high emissions and energy consumption. Based on provincial panel data from China’s Yangtze River Economic Belt from 2009 to 2020, this paper uses a super-SBM, which includes undesirable outputs and is combined with the Global Malmquist-Luenberger (GML) index, to measure and analyze the regional logistics efficiency. Panel regression and threshold regression models are used to test the impact of formal and informal environmental regulations on logistics efficiency, rather than the common single perspective. The results indicate that: (1) Environmental regulation has a significant impact on the overall logistics efficiency of the Yangtze River Economic Belt during the study period, and there is a problem of regional development incongruity. The maximum difference in logistics efficiency between provinces is 0.5637. (2) The impact mechanism of formal and informal environmental regulations differs, and each percentage of informal environmental regulation has a promotion effect on logistics efficiency that is 0.0827% higher than that of formal environmental regulation. (3) Formal environmental regulation has a single threshold effect on logistics efficiency, whereas informal environmental regulation has a double threshold effect, demonstrating that overregulation can have the opposite effect. Based on different regulatory tools, this paper makes pertinent recommendations to promote the coordinated development of the logistics industry’s economic and environmental benefits in the Yangtze River Economic Belt.