As data becomes an institutionalized production factor, data factor marketization may fundamentally reshape regional innovation systems. This study investigates whether and how data factor marketization influences regional innovation performance from an institutional perspective. Using provincial panel data from 2000 to 2023 and exploiting a staggered difference-in-differences (DID) design, this study identifies the impact of institutionalized data exchange on regional innovation. The results indicate that data factor marketization significantly promotes regional innovation performance. Mechanism analysis shows that the effect operates by accelerating technological iteration and strengthening the transformation of research achievements, thereby enhancing knowledge renewal and commercialization efficiency. Heterogeneity analysis further reveals that the innovation-enhancing effects are stronger in regions with higher economic development, higher levels of marketization, greater R&D input, and higher baseline innovation capacity, and are more pronounced in the eastern and southern regions. These findings suggest that data factor marketization complements existing innovation systems, but its impact depends on whether regions have sufficient institutional capacity to convert digital market reforms into tangible innovation outcomes.