Under the dual carbon goals, digital logistics offers a new green development path for the manufacturing industry. Using the provincial panel data from 2013 to 2021, digital logistics levels was measured and manufacturing’s green total factor productivity (GTFP) via EBM-GML was assessed. Furthermore, fixed effects models and mediation effect models were employed to explore the direct and indirect relationships between digital logistics and the green development of the manufacturing industry. The research indicates that digital logistics enhances resource allocation, structural optimization, and green production. Moreover, the application of digital logistics has a significant impact on enhancing the total factor productivity of the manufacturing industry. Digital logistics can elevate the level of green development in the manufacturing industry through three avenues, such as efficiency transformation, optimization of energy consumption structure, and enhancement of technological innovation capabilities.