The establishment of a low-carbon transportation system (LCTS) holds prominent importance in advancing modern transportation development and achieving green growth. Employing the LCTS pilot policy as a shock to green transportation construction in China, we investigate its influence on carbon emission efficiency (CEE) using urban panel data from 2006 to 2021. Results based on difference-in-differences (DID) show that LCTS contributes to increasing CEE following such a pilot policy. This finding still holds after we perform a propensity score matching DID method, double machine learning, instrumental variable method, heterogeneous treatment effect, and other robustness checks. Meanwhile, the mediation analysis shows that the increased CEE can be accounted for by spurring green innovation activities. Moreover, the moderation outcomes reveal that FinTech exerts a positive moderating influence on the increased impacts of LCTS on CEE. Heterogeneity analysis shows that LCTS's impact on CEE varies by region and development level. Overall, our research stresses the importance of green transportation construction in shaping CEE, which has significant practical and theoretical implications for scholars and policymakers.