In the post epidemic era, small and medium-sized enterprises can ensure employment only if they achieve comprehensive economic recovery through innovation. Based on the innovation survey data, this paper explores the barriers to innovation and the factors that affect innovation investment. It is found that cost, market and institutional barriers are important factors that hinder innovation, but only market barriers are dominant factors. By contrast, knowledge barriers do not prevent firms from innovating, but rather prevent them from investing in innovation. Comparing small and medium-sized enterprises with large companies, we find that small and medium-sized enterprises are more affected, especially the cost factor. These findings suggest that the participation of enterprises in innovation can be encouraged by broadening the range of policy instruments. Once enterprises enter into innovation, knowledge barriers should be reduced.