Abstract: Value-added tax transformation aims to promote industrial upgrading and economic restructuring through tax reduction, but there is little VAT transformation literature studying the impact of reform on enterprise’s R&D. And the existing research on tax policy and R&D investment mainly focuses on corporate income tax. In theory, VAT transformation can stimulate R&D investment by mitigating the internal financing constraints of enterprises, but this effect is affected by the heterogeneity of enterprises. This paper analyzes the influence of VAT transformation on the R&D behavior in different types of enterprises based on group perspective. Empirical study finds that, without distinction of organization forms, there is no evidence of VAT transformation’s significant impact on R&D investment; after considering organization forms, we find that VAT transformation significantly stimulates business group’s R&D investment, and private group’s R&D investment is significantly higher than state-owned group; further analysis of private group reveals that agency cost restrains its R&D investment; Moreover, private group’s long-term growth rates of return is significantly higher than that of other firms as a result of more R&D investment. This paper not only enriches the literature of value-added tax reform, but also can provide reference for the reform of “to replace the business tax with a value-added tax”.