<p>How can the growth potential of carbon productivity be released through the optimization of innovative spatial structure? Polycentricity serves as a valuable entry point for our study. From the perspective of structure-scale-benefit, this paper integrates innovative polycentricity, innovative scale, and carbon productivity into the same analytical framework. It empirically examines the impact of innovative polycentricity on carbon productivity and its pathways, and verifies the moderating role of innovative scale using Chinese provincial-level panel data from 2000 to 2020. The empirical results suggest that innovative polycentricity has a positive U-shaped effect on carbon productivity, with a short-term dampening effect and a long-term facilitating effect. This result remains consistent after the robustness test. Innovative polycentricity affects carbon productivity mainly through pathways that influence resource allocation and technological achievement commercialization. Innovative scale positively moderates the relationship between innovative polycentricity and carbon productivity. A larger innovative scale allows a region to reach the inflection point of polycentricity more quickly and maximize the long-term impact of innovative polycentricity on carbon productivity. This paper offers a new perspective for studying the low-carbon effects of innovation and has implications for the sustainable development of China and other countries.</p>