Based on provincial-level panel data in China from 2009 to 2022, this study empirically examines the impact of government audits on financial agglomeration. It employs mediation effect models and panel threshold effect models to explore the role of industrial structure upgrading in this relationship. The findings reveal that government audits significantly foster financial agglomeration on a national scale, albeit with regional variations. Specifically, there is a pronounced positive effect in regions with high financial agglomeration levels, while no significant impact is observed in regions with low levels; Industrial structure upgrading plays a significant partial mediating role in the process by which government audits affect financial agglomeration; Furthermore, industrial structure upgrading exhibits a dual-threshold effect, and as industrial upgrading intensifies, the positive effect of government audits on financial agglomeration becomes increasingly significant. Consequently, it is essential to strengthen the role of government audits and promote industrial structure upgrading to enhance the positive contribution of financial agglomeration to economic development.