This paper explores the influence of fiscal structural change on industrial structure from the perspective of inter-industry relations. The inter-industry fiscal structural change significantly accelerates industrial structural change and promotes industrial structure upgrading. The main mechanism lies in the inter-industry different allocation of fiscal and tax resources and more resources devoted to industries with higher dependence on external finance. The performance of fiscal structural change is restricted by institutional constraints and marketization level and is featured by heterogeneity, shown by the facts as follows: on account of the differences in institution constraints, the effect of subsidy-based structural change on industrial structure is remarkably weaker than the one of tax-based structural change; based on the differences in marketization level, the effect of fiscal structural change on industrial structure change varies across areas, higher in the West China and lower in the East China, while the effect on industrial structure upgrading mainly concentrates in the East China.