Data science can promote the intelligence of national governance methods, and enhance the efficiency and effectiveness of national governance through the incorporation of big data collection and processing and intelligent decision-making system. This paper systematically utilizes a variety of methods to study and analyze the optimization strategy of the national governance system of data science under the Marxist perspective. It evaluates the effect of the digital transformation of the governance system implemented in place A by constructing a national governance evaluation index system, and provides focus indicators in the transformation process using fuzzy hierarchical analysis. The average coefficient of variation squared for Digital infrastructure, Agricultural digitization, and Governance digitization is 0.734, 0.876, and 0.775, respectively, which provides a better discriminatory ability. Experts showed different emphasis on different indicators, with “Product network sales rate” scoring the lowest at 78.282. After implementing the governance system optimization strategy, the ecological level of Site A has been increasing year by year. And the national governance system based on data science gets consistent satisfaction from residents, with a comprehensive rating of about 4.26. This paper provides theoretical support and empirical enlightenment for the optimization of the national governance system in the new era.