Abstract: Using the Crop Research Institute of Fujian Academy of Agricultural Sciences（hereinafter referred to as “Crop Institute”）as a case, this longitudinal case study compares management practices and outcomes between 2014−2016（pre-system implementation）and 2020−2022（post-system implementation）. Results demonstrate that through four key mechanisms—process optimization, power checks, risk prevention, and information transparency—the Crop Institute achieved significant improvements in research funding utilization efficiency across multiple dimensions:（1）Compliance: A notable reduction in fund irregularities and audit issues;（2）Efficiency: Substantial increases in budget execution rates and reimbursement efficiency, shortened procurement cycles, and sustained high staff satisfaction;（3）Cost-effectiveness: Effective control of public operational costs and rationalization of resource allocation;（4）Impact: The internal control system created a stable environment, driving exponential growth in per capita research achievements, authorized patents, and technology transfer funding. The study suggests that systematic institutional development through internal control frameworks has facilitated a coordinated leap from extensive to refined management of human, financial, and material resources, establishing a solid managerial foundation for scientific research output. This study provides an empirical approach to resolve the dilemma of "overemphasis on application and neglect of management" in agricultural research institutions.