Abstract: Drawing on the technological heterogeneity framework, this paper develops a common-frontier efficiency model that incorporates undesirable outputs to estimate the ecological efficiency of production and waste treatment at 47 Chinese logistics hubs over 2011−2021. It then examines the key factors driving efficiency losses. The results show that eco-efficiency has exhibited an overall upward trend: the average scores for the production and waste-treatment stages were 0.698 and 0.593, respectively. Significant heterogeneity exists across hub types, and the technological gap between the two stages has widened over time. Overall ecological inefficiencies stem from both technological shortcomings and managerial deficiencies. Moreover, regression analysis indicates that urban economic level and environmental regulation significantly boost eco-efficiency; in contrast, energy structure and OFDI exert a significant negative effect, whereas industrial agglomeration and government support show no significant impact.