Improving the logistics ecological efficiency (LEE) has become a significant part of ensuring a sustainable development and tackling environmental pollution. Previous studies in the logistics industry seldom considered air pollutants and the association of spatial information. Therefore, innovatively considering SO2, NOx, and PM, this study adopted the Super-SBM-Undesirable model to calculate the LEE of 30 provinces in China from 2004 to 2017, and thereafter, developed information-based matrix to explore its influencing factors by using the spatial Dubin model. The results indicated that: (1) The overall LEE during the study period was low, presenting a U-shaped trend of an initial decrease and subsequent rise, and significant regional differences with the decreasing gradient pattern of the “Eastern-Central-Western.” (2) A spatial directionality distributed from the northeast to southwest, and a significant spatial autocorrelation were observed. (3) The industrial structure had the greatest positive influence on the local LEE, followed by the urbanization level, technology innovation level, environmental regulation, while the energy intensity was identified as the main inhibiting factor, followed by the economic level, energy structure and opening level. (4) The LEE had a significant positive spillover effect; the energy intensity and environmental regulation positively affected the LEE in neighboring areas, while the opening level had negative impacts. In addition, policy recommendations for enhancing the LEE were made.