<p>China’s low-carbon transition requires the effective allocation of green innovation factors, yet their spatial imbalance constrains national innovation efficiency. This study examines how the agglomeration of green finance reshapes the flow of green innovation factors by distinguishing between the level and speed of agglomeration. The results show that moderate agglomeration of green finance promotes the interregional circulation of green innovation factors, while excessively rapid agglomeration hinders their spillover effects. Furthermore, the development of technology markets and regional economic conditions are found to exert significant moderating influences, revealing a nonlinear relationship between green finance agglomeration and green innovation factor flow. These insights enrich the understanding of interactions between finance and innovation during economic restructuring, and offer policy insights for promoting balanced green development.</p>