Climate change poses unprecedented challenges for humanity. Reducing carbon intensity is an inevitable choice for tackling climate change and promoting sustainable development. China has made some emission reduction commitments in the international community to promote the decoupling of China’s economic development from carbon emissions. The realization of the industrial structure from the “single-wheel drive” of the manufacturing to the “two-wheel drive” economic development model of the service industry and the manufacturing has become a key measure to achieve China’s economic intensive development. According to resource misallocation situation in different regions, this paper explored the impact of the collaborative agglomeration between producer services and manufacturing (hereinafter referred to as industrial co-agglomeration) on carbon intensity. The research results show that the carbon intensity is decreasing year by year, and the degree of intensification of China’s economic growth continues to increase. Moreover, the effect of industrial co-agglomeration to promote carbon emission reduction is significantly limited by the degree of misallocated resources, and there is a double threshold effect. Specifically, in areas where resource allocation is reasonable, industrial co-agglomeration can produce significant agglomeration effects and promote carbon intensity reduction. Once the degree of misallocated resources exceeds a threshold level, the agglomeration effect will turn into a crowding effect, resulting in an inability to reduce carbon intensity. We comprehensively analyzed the driving factors for reducing carbon intensity and proposed policy pathways for achieving China’s carbon intensity target.