Based on the theory of the innovation helix framework, this article selects Israel, which has a reputation as an innovative country, and China, which is developing rapidly, as the research objects. Analyzed the construction of the national innovation system of Israel and China. And compared the national innovation systems of the two countries from different dimensions such as the roles of governments, enterprises, universities, and scientific research institutions in the national innovation system, the coordination operation capability of the innovation system, and innovation capabilities and efficiency. This shows the Similarities and differences in the construction of the national innovation system of these two countries in terms of goals, dominant forces, and social environment.