To improve independent innovation ability, China has explored a unique form of R&D organization called the New R&D Institute (NRDI). The spillover effect of NRDIs in the region arouses curiosity about what exactly drives its innovation performance. After clarifying the NRDI concept and its characteristics, this study studies Nanjing, a typical city with the rapid development of NRDIs in China, to empirically explore the impact mechanism of NRDI development in their start‐up period. The study uses panel data from 103 NRDIs spanning 10 quarters from the third quarter of 2018 to the fourth quarter of 2020. Our analysis reveals that R&D investment, government support, research infrastructure, and angel investment have mixed impacts on the revenue, innovation, and enterprise incubation of NRDIs. Specifically, resource inputs such as R&D staff, R&D service platforms, and R&D expenditures boost the revenue growth of NRDIs. In contrast, only a few inputs play an important role in NRDIs’ innovation and enterprise incubation, including service platforms, capital investment from high‐tech parks, and angel funding. The early development of NRDIs has four features. (1) It is driven more by material capital (R&D expenditure) than by human capital (R&D staff). (2) It relies more on government support rather than institution investment. (3) Research infrastructure has specific significant effects on the innovative output of NRDIs. (4) Angel investment is critical to promote technological innovation and business incubation. Most of the input elements have not yet been very effective in the innovation and incubation of NRDIs. Our research offers essential insights for understanding the innovation mechanism in NRDIs and promoting their healthy development.