Abstract: “SRDI” small and medium-sized enterprises (S-SMEs) are an important vehicle for implementing innovation-driven strategies. In view of the lack of research on the micro-level of S-SMEs' innovation performance in academic circles, this paper examines the significant key factors and configuration effect that influence S-SMEs' innovation performance from the perspective of complex causal effect analysis, mixing NCA, empirical regression and QCA methods, and refines the corresponding improvement paths. It is found that (1) R&D capability, financing environment and market competitiveness significantly affect the innovation performance of S-SMEs; (2) there are five configuration paths that enhance the innovation performance of different types of S-SMEs; (3) when financing is blocked, either small-scale production or improving their own market competitiveness can enable S-SMEs to maintain a high level of innovation performance target. This paper attempts a new way of thinking of complex causal effect analysis, which provides some theoretical and practical references for the study of S-SMEs' innovation performance in the future.