This study employs spatial durbin model (SDM) and spatial mediation model to empirically investigate the relationship between logistics agglomeration (LA) and logistics eco-efficiency (LEE), as well as the transmission mechanism role of technological innovation (TI) and advanced industrial structure (AIS), using panel data on inter-provincial logistics in China from 2008 to 2020. The findings indicate a U-shaped relationship between LA and LEE. The early development of LA in China was accompanied by environmental sacrifices. Further analysis of the curves reveals that LA has spatial spillover effect on LEE. That is, insufficient concentration of LA has a siphon effect on the LEE of surrounding areas, whereas appropriate concentration of LA has a radiation effect on the LEE of surrounding areas. Spatial mediation analysis indicates that enhancing TI and developing AIS are essential channels through which LA bolsters LEE. Additionally, this study innovatively incorporates topography ruggedness and altitude as instrumental variables to account for potential endogeneity issues in the empirical model. Theoretical and practical significance is attributed to this research for China's logistics industry, particularly shedding light on the optimization of efficiency and long-term improvement of LEE through spatial reform via agglomeration zones.