Innovation activities in manufacturing enterprises in emerging countries face a dilemma in simultaneously implementing exploitation and exploration innovation due to a lack of synergy capacity. Building upon the theories of dual innovation synergy and strategic flexibility, this study proposes a mechanism for achieving dual innovation synergy through digitalization, which can enhance innovation performance. We argue that digitalization improves innovation performance via dual innovation synergy. Additionally, we suggest that strategic flexibility moderates the relationship between digitalization and innovation performance by coordinating innovation strategy and other strategies. The results indicate a positive impact of digitalization on innovation performance, mediated by dual innovation synergy. Furthermore, an increase in strategic flexibility enhances the positive effect of dual innovation synergy on innovation performance, thereby amplifying the positive influence of digitalization on innovation performance through dual innovation synergy. This research contributes to the existing literature on the impact of digitalization on innovation performance by emphasizing the crucial role of dual innovation synergy and strategic flexibility in innovation management.