Breakthrough innovation is a core driving force in advancing Chinese modernisation, while the efficiency with which financial resources are allocated across space directly determines how effectively financial services can empower technological innovation. Drawing on panel data for A-share listed firms in Shanghai and Shenzhen from 2013 to 2023, this study systematically examines the relationship between financial geographic agglomeration and firms’ breakthrough innovation, as well as the underlying mechanisms. The empirical results show that financial geographic agglomeration significantly reduces the intertemporal similarity of firms’ patented technologies and exerts a significant positive effect on breakthrough innovation. Easing financing constraints, reducing information asymmetry between banks and firms, and increasing the supply of patient capital constitute key transmission channels through which financial geographic agglomeration delivers its innovation-enhancing impact. Moreover, these effects are more pronounced among digital firms, firms in regulated industries, and heavily polluting firms. By extending the theoretical framework on financial agglomeration and corporate innovation from the perspective of the “micro-level accessibility” of financial space, this study clarifies the internal logic through which financial geographic agglomeration affects breakthrough innovation. The findings provide robust empirical evidence and policy implications for optimising the spatial allocation of financial resources, improving the system of finance for science and technology, and enabling the development of new quality productive forces through finance.