Abstract: This study compares and analyzes the sophistication of chronic disease prevention and control organizational systems in Jiangsu and Zhejiang provinces, exploring their relationship with disease control effectiveness to inform further optimization of chronic disease management in these regions. Using policy documents from 2009 to 2023, the study quantitatively assesses system sophistication across three dimensions: organizational structure robustness, coordinating authority legitimacy, and role clarity. Indicator values were assigned through keyword extraction and field analysis. Spearman correlation analysis and stepwise regression analysis were employed to examine the association between system sophistication and prevention outcomes. Spearman correlation results indicate an overall upward trend in the sophistication of chronic disease prevention and control organizational systems in both regions. Stepwise regression analysis reveals that the most influential predictor of prevention effectiveness in both regions is the clarity of responsibilities. This study concludes that the sophistication of the chronic disease prevention and control organizational system is a crucial foundation for enhancing regional prevention and control effectiveness. It is recommended that localities further optimize organizational structures, strengthen coordination mechanisms, and clarify responsibilities and divisions of labor based on their actual conditions to enhance comprehensive chronic disease prevention and control capabilities.