National modern agricultural industrial parks are the core carriers for promoting agricultural modernization. Clarifying their spatial differentiation patterns is of great significance for revealing the efficiency of resource allocation and promoting coordinated regional development. Based on the data from 338 national modern agricultural industrial parks in China, this study uses methods such as the nearest neighbor index, Voronoi spatial statistics, and spatial autocorrelation to identify their spatial distribution characteristics, and adopts the XGBoost–SHAP model to explore the nonlinear effects of driving factors. The research found the following: (1) The parks exhibit a distinct “sparse west–concentrated middle–dense east” agglomeration pattern aligned with China’s Hu Huanyong Line agro–economic divide. (2) At the municipal level, four high-density cores emerged in central-eastern regions with “dual hot spots–gradient diffusion” characteristics. (3) Farmers’ professional cooperatives and transportation accessibility are the most consistent fundamental driving elements, reflecting the transition of the development momentum of contemporary agriculture from “resource dependency” to “circulation dependence.” Heterogeneity analysis shows elevation, cooperatives and rural income differentially drive agglomeration across regions, with elevation constituting a universal constraint. (4) While regional development and mechanization show adaptive synergy, excessive urbanization generates a distinct “non–agriculturalization” crowding–out effect on agricultural development.