Root innovation is a new innovation paradigm that deeply integrates scientific and technological innovation with industrial innovation， and it is an important path to achieve high-level scientific and technological self-reliance and self-improvement. Based on the strategic practice of contemporary innovation development， this paper believes that root innovation is a systematic innovation that combines the breakthrough of principle technology， the reconstruction of industrial market and the driving force of value ecology. Based on this， the paper analyzes the underlying logic of root innovation in cognitive， technological， and value dimensions， and strives to enrich the theoretical spectrum of innovation economics by constructing a theoretical analysis framework for root innovation， providing a new research perspective for the construction of the national innovation system and the high-quality development of industries. In the process of Chinese path to modernization， we need to further deepen the understanding of the regularity of root innovation and fully release its powerful driving force for social and economic development.