Building a unified national market requires continuously improving the consistency of regional policies and rules. This paper takes the R&D subsidy policy as an example to systematically analyze the dual effects of R&D subsidy competition from two aspects: regional technological innovation and regional industrial similarity, and then reveals the internal relationship between building a unified national market and improving regional-policy coordination. It is found that R&D subsidies not only promote technological innovation and economic growth in the region, but also significantly inhibit technological innovation and economic growth in other regions. Therefore, they have become an important policy tool for local governments to promote regional innovation and participate in regional competition in the context of high-quality development. Competition to increase R&D subsidies, also known as R&D subsidy Competition, can promote technological innovation and economic growth in the region, but it will also motivate local governments to continuously improve the degree of regional industrial similarity. On the contrary, if the central government can coordinate the R&D subsidy standards between regions, R&D subsidies can not only promote technological innovation and economic growth, but also stimulate local governments to carry out regional industrial division of labor and reduce the degree of regional industrial similarity. Therefore, building a unified national market requires improving the consistency of regional policies.