With tax and subsidy as a focal point, this paper explores the effect of the fiscal resource reallocation of manufacturing industry on industrial structure, and evaluates the effect on the structural bonus. We find that, firstly, there is obvious fiscal resource reallocation in the manufacturing industry, especially the reallocation of subsidy; secondly, generally speaking, the reallocation of subsidy significantly promotes the factor flow towards the industry with higher productivity or productivity growth, conforming to the “Structural Bonus Hypothesis”, while the effect of the tax reallocation is negative; thirdly, the exploration of the institutional constraints shows that, both of fiscal decentralization and marketization can strengthen the positive effect of fiscal resource reallocation and weaken its negative influence.