Coordinated regional development is an important issue for China in the new era, and the influence of innovation ability on regional economic development is increasing, but the current regional innovation is characterized by an increasingly obvious “dualization” effect. In this paper, by constructing innovation efficiency, science and technology innovation, innovation culture, and innovation policy as the four key subsystems of regional innovation effect, and using system dynamics to establish a regional innovation effect model, Wuhan and Enshi as the representatives of central city and non-central city, selecting the data from 2014 to 2021, and adopting different parameters to simulate the evolution trend of the innovation effect, it is concluded that the growth rate of industrial enterprises and the intensity of R&D expenditures have increased, and the innovation effect has become more and more obvious, which is the most important issue in the new era of China’s development. It is also concluded that the growth rate of industrial enterprises and the intensity of R&D expenditure are the key factors influencing the innovation effect of central and non-central cities, and suggestions are made for optimizing the “dualization” effect of regional innovation.