Small and medium-sized enterprises (SMEs) are constrained by financial and scale limitations, and it is often difficult for them to “do it alone” on the road of innovation. The status quo of SMEs’ weak innovative capacity has been highlighted in recent years. It is of great significance to discuss how to use policy tools to promote innovation in SMEs. This paper constructed a DID model based on the data of listed companies on SEM and GEM boards from 2013 to 2020, and examined the micro-mechanism of the impact of pretax additional deduction policy for R&D expenditure on SMEs’ innovation ability from the perspective of cooperative innovation. The study found that: (1) The implementation of pretax additional deduction policy for R&D expenditure can significantly enhance the innovation capacity of SMEs, which is reflected in the improvement of innovation continuity, innovation quality and total factor productivity. (2) Mechanism analysis shows that the mechanism by which pretax additional deduction policy for R&D expenditure affects SMEs’ innovation capacity is to promote collaborative innovation among firms. (3) The policy reduces the search costs for collaborative partners and risk costs for knowledge leakage by adding the deduction of costs related to collaborative innovation, thus enhancing the willingness of SMEs to collaborate and innovate. (4) The promotional effect of pretax additional deduction policy for R&D expenditure on SMEs’ collaborative innovation is more pronounced in highly digitized firms, and firms in highly technology-intensive industries and in regions with better science and technology intermediation and innovation platforms have benefited more from the policy benefits. This paper enriches the theoretical and empirical research on SMEs’ innovation policies, and will provide important insights into the promotion of innovative capacity through collaborative innovation in SMEs.