China has long been confronted with pronounced disparities in the number of participants across its five employee social insurance programs and with fragmented administrative procedures. To enhance the operational efficiency of the social insurance system, a policy of unified enrollment and contribution collection for the five employee social insurances—commonly referred to as the “Five-insurance Integration”—has been progressively rolled out across regions. This integration has evolved through two major stages: an initial stage of internal integration within human resources and social security (HRSS) departments, and a subsequent stage of coordinated integration involving tax authorities, HRSS departments, and healthcare security (medical insurance) departments. “Five-insurance Integration” will raise corporate social insurance contributions, which may impede corporate innovation through a labor-cost effect, or may reduce overall costs and foster corporate innovation through a factor-substitution effect (capital substituting for labor) and an efficiency-enhancing effect. To empirically determine the net impact on corporate innovation, this paper employs a DID approach using data on A-share listed companies from the CSMAR database over the period 2007-2023. The results show that “Five-insurance Integration” significantly promotes corporate innovation. The ratio of R&D expenditure to operating revenue increases by 0.305-0.609 percentage points, indicating that the factor-substitution and efficiency-enhancing effects outweigh the labor-cost effect. This policy effect works primarily through two channels—raising corporate social insurance compliance and upgrading human capital, and is characterized by short-term cash-flow pressures coupled with medium-to-long-term improvements in resource allocation. Heterogeneity analysis further demonstrates that the policy effect is more pronounced in eastern regions, SMEs, non-SOEs, and regions with non-full-responsibility collection by tax authorities. Based on the findings, it is recommended that China strengthen the synergy between the “Five-insurance Integration” policy and policies such as employment stabilization, and advance inter-departmental information sharing and administrative service consolidation, so as to further amplify the effectiveness of “Five-insurance Integration”, and provide robust support for corporate innovation and the sustainable development of the social insurance system.