Against the backdrop of China’s innovation-driven development strategy and deepening financial reforms, the rational allocation of financial responsibilities between central and local governments has become a critical institutional factor influencing regional innovation capacity. Clarifying the impact mechanisms and effects of financial decentralization on regional innovation holds significant practical implications for optimizing government-market relations and building high-level regional innovation systems. Existing research predominantly focuses on the innovation effects at the micro level of enterprises or fiscal decentralization, with insufficient exploration of the innovation mechanisms and structural characteristics of financial decentralization at the regional macro level. Therefore, how to effectively leverage the “visible hand” of financial decentralization to promote the “invisible hand” of market resource allocation in advancing regional innovation holds significant theoretical value. Based on panel data from 31 Chinese provinces spanning 2006 to 2022, this study constructs a multidimensional index of financial decentralization. Employing a fixed-effects model, it systematically identifies the impact of financial decentralization on regional innovation and examines its transmission mechanisms through three primary channels: government function, financing constraints, and resource allocation. The results indicate that financial decentralization significantly enhances both regional innovation capacity and output. Financial decentralization not only effectively promotes the execution of governmental innovation functions but also corrects regional resource misallocation. By channeling financial resources from inefficient sectors to innovation-driven fields and alleviating corporate financing constraints—particularly improving credit accessibility for small and medium-sized technology enterprises—financial decentralization elevates regional innovation levels. Further analysis reveals that: both decentralization from the central to local governments (Type I Decentralization) and decentralization from the government to the market (Type II Decentralization) foster regional innovation development; implicit financial decentralization demonstrates positive effects, whereas explicit financial centralization significantly inhibits innovation; fiscal decentralization exhibits a substitution effect on financial decentralization; and the innovation-promoting effect of financial decentralization is more pronounced in regions with weaker social capital and lower educational investment, suggesting that institutional empowerment can partially compensate for deficiencies in inherent regional conditions. Compared with previous studies, this paper makes the following contributions. First, it deconstructs the analytical hierarchy of financial decentralization and innovation studies, systematically reveals a new mechanism of institutional-spatial adaptability, and broadens the research perspective on the economic consequences of financial decentralization. Second, it uncovers how the multidimensional attributes of financial decentralization differentially impact regional innovation. By analyzing the effects of specific decentralization characteristics on regional innovation and comparing outcomes across different levels of decentralization, this study refines the understanding of how decentralization reforms influence regional innovation. Third, it refines the chain of influence through which financial decentralization impacts regional innovation. By systematically mapping its tripartite transmission mechanism—involving government innovation functions, resource misallocation, and financing constraints—it clarifies the logical pathways of financial decentralization’s effects on regional innovation, providing a theoretical grounding for regional innovation studies. The theoretical contribution lies in broadening the analytical dimensions of financial decentralization, revealing its dual-channel mechanism through government and market to influence regional innovation. This provides new empirical evidence for understanding the relationship between decentralization reforms and innovation performance within China’s institutional context. Recommendations include deepening financial decentralization reforms “from local governments to the market,” institutionalizing implicit decentralization, implementing differentiated regional decentralization strategies, and strengthening fiscal-financial policy coordination to maximize the innovation-driving efficacy of financial decentralization.