Data Envelopment Analysis (DEA) is a widely adopted non-parametric technique for evaluating R&D performance. However, traditional DEA models often struggle to provide reliable solutions in the presence of data uncertainty. To address this limitation, this study develops a novel robust super-efficiency DEA approach to evaluate R&D performance under uncertain conditions. Using this approach, we analyze the R&D performance of industrial enterprises across 30 Chinese provincial regions from 2018 to 2022. The empirical results reveal a notable decline in R&D performance during 2018-20, driven by external shocks such as trade conflicts and the pandemic, followed by a gradual recovery post-2020, a trend that remains consistent under varying levels of data perturbation. Regional analysis highlights substantial disparities in R&D performance across Chinese regions. Comparative analysis further demonstrates the proposed model's advantages in feasibility and computational efficiency. Based on the empirical analysis, we provide several policy implications. While rooted in the Chinese context, this paper contributes both methodologically through its robust DEA framework for handling uncertainty, and empirically by offering valuable insights into improving R&D performance in diverse national and organizational settings.