With the rapid development of society and technology, the physical health of university students has become a critical concern, influencing both individual well-being and the national talent pool. This study employs an improved K-means algorithm integrated with machine learning models to analyze university students’ fitness data and develop personalized health intervention strategies. The enhanced K-means algorithm overcomes the limitations of traditional clustering approaches, leading to improved clustering accuracy and stability. Machine learning models—including Random Forest, decision trees, Gradient Boosting Trees, and logistic regression—were utilized to validate the clustering outcomes and to identify key health indicators associated with different student groups. Based on the clustering and model analysis, targeted intervention programs are proposed, such as strength training for groups with low muscular explosiveness, endurance training for those with stamina deficiencies, and flexibility exercises for groups exhibiting limited mobility. This integrated analytical framework provides a scientifically grounded tool for comprehensive health assessments and offers actionable, data-driven recommendations for student health management. Future research will focus on optimizing algorithmic performance, enhancing data diversity, and broadening the application scope to further improve the effectiveness and feasibility of health interventions.