Due to increased government investment in university education funds, there have emerged significant challenges and complexities in managing and utilizing scientific research funds within universities. To address these issues and ensure accurate risk assessment in scientific research project implementation, we propose a comprehensive evaluation system that combines game theory and grey clustering. Firstly, we establish a risk assessment index system based on industry standards and data analysis. Then, we apply the game theory combination weighting algorithm to optimize the balance between subjective and objective weights, resulting in a final comprehensive weight. Subsequently, we assess the project's risk level using the grey clustering method. The experimental results confirm the system's effectiveness in evaluating and ranking risks. In summary, our approach addresses the challenges associated with managing university research funds amidst increased government funding, offering a robust system for risk assessment and ranking.