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In the evaluation activities of various economic systems, the selection of the design of the indicator system is often subjective. In practice, these principles tend to focus on formalization, and there are big differences with the process of selecting specific indicators. The regional economic development has entered a critical period of transition to a high-quality development stage, but the contradiction of insufficient regional economic imbalance development is still a constraint factor for the high-quality development of the regional economy. Based on the fractional differential equation analysis method, it expounds the mechanism of high-quality development of regional economy from 10 dimensions such as GDP, tertiary industry added value, local fiscal revenue, scientific and technological innovation, and market mechanism. Combining the ideas of the new development concept to promote the high-quality development of regional economy, the system is evaluated by fractional differential equations. The best indicator system framework was selected to build an economic system impact factor indicator system. According to the SEM analysis results, the weights of each index are determined. [ABSTRACT FROM AUTHOR]