The impact of industrial co-agglomeration (ICA) on green total factor productivity (GTFP) has garnered considerable academic attention. However, there remains a gap in research systematically investigating how ICA affects China’s GTFP within the framework of green development, specifically by analyzing transmission mechanisms, regulatory mechanisms, and spatial spillover effects. To address this gap, this study utilizes panel data from 283 Chinese cities, spanning the years 2006 to 2020, and conducts both theoretical and empirical analyses to examine ICA’s influence on GTFP through these three mechanisms. Our findings indicate that ICA significantly enhances GTFP by alleviating the mismatch of capital and energy factors but does not improve GTFP by addressing labor mismatches. Furthermore, when the intensity of local government competition exceeds a threshold of 14.3825, the positive impact of ICA diminishes, whereas an environmental regulation intensity above 0.4381 strengthens ICA’s positive effect on GTFP. ICA was found to substantially increase local GTFP and generate positive spatial spillover effects on surrounding cities within a 100 km radius. Co-agglomeration of both high-end and low-end producer services with manufacturing boosts local GTFP, while co-agglomeration of low-end producer services with manufacturing also enhances GTFP in adjacent cities. In megacities, ICA positively influences both local and nearby GTFP, whereas in large cities, ICA tends to suppress GTFP in neighboring areas. Additionally, with the exception of the Middle Yangtze River and Pearl River Delta city clusters, ICA in urban clusters enhances local GTFP; ICA in the Middle Yangtze River cluster promotes GTFP in neighboring areas, whereas ICA in the Chengdu–Chongqing cluster inhibits neighboring GTFP.