Based on the perspective of structural change, this paper analyzes the short-term crowding effect and long-term human capital effect of social security contributions on enterprise innovation using data from non-financial companies listed on A-shares in China from 2004 to 2021, and further explores the innovative effect of distorted social security contribution structures. Research has found that there is a positive U-shaped relationship between the most suitable social security payment structure of enterprises and the changes in their factor endowment structure; The deviation of corporate social security payment structure inhibits enterprise innovation; There are structural differences in the impact of deviation on innovation among different types of enterprises; Excessive social security contributions inhibit enterprise innovation.