The carbon emissions trading system (CETS) is a crucial market-based tool aimed at achieving the goals of “carbon peaking” and “carbon neutrality”, and plays a pivotal role in promoting the green development of the logistics industry. The green total factor productivity (GTFP) of the logistics industry is a key indicator used to measure the green development level of the logistics industry. The research on the CETS and the GTFP in the logistics industry(LGTFP) is currently lacking. Accurately assessing the impact of CETS on LGFP is crucial for improving the construction of the CETS and promoting the green transformation of the logistics industry. Utilizing a combined approach of system dynamics and econometrics, this study examines the effects of CETS on the LGFTP. In this study, the impact mechanism of CETS on the LGTFP is analyzed by constructing a causal relationship diagram using system dynamics theory. And then, we construct a multi-period differencein- difference (DID) model using panel data from 30 Chinese provinces spanning from 2010 to 2020 to verify the impact of CETS on LGTFP. The findings reveal that: (1) CETS significantly promotes LGTFP, and this conclusion is consistent even after conducting robustness tests. (2) Green technological innovation is identified as the primary influencing mechanism of CETS in enhancing LGTFP, while industrial upgrading does not play a positive mediating role, contrary to established studies. (3) Heterogeneity analysis reveals that CETS has a significant promotion effect on LGTFP in central and western regions, and resource-based provinces, but not yet in eastern regions and non-resource-based provinces. Based on the empirical analysis, we propose relevant policy recommendations to improve China’s CETS and promote the improvement of LGTFP.