Introduction: In higher education, the relationship between engagement in sports learning and intrinsic motivation is critical. Although sport benefits health and academic performance, its long-term motivational mechanisms remain unexplored. This study examines how intrinsic motivation influences sports participation, its trends, and its implications for university physical education and student development. Method: This study conducted a 1.5-year longitudinal survey in three phases (T1, T2, and T3) with 365 university students. Data were coded and analyzed using SPSS 26.0 and Mplus 8.0. SPSS 26.0 assessed the stability of sports engagement and intrinsic motivation using item, factor, bias, correlation, and repeated-measures ANOVA analyses. Mplus 8.0 applied cross-lagged analysis to examine the predictive relationships among intrinsic motivation, cognition, behavior, and emotional engagement. Results: The results indicate that: 1) Intrinsic motivation and sports engagement decrease from T1 to T3, with emotional involvement greater at T1 than at T2 and T3, and cognitive involvement greater than at T3; 2) Intrinsic motivation correlates positively with all types of engagement, being strongest with emotional engagement. 3) It predicts subsequent cognitive and behavioral engagement, but affects emotional engagement only from T2 to T3, with a greater influence on behavioral engagement from T2 to T3 than from T1 to T2; 4) Prior behavioral and emotional engagement enhances subsequent intrinsic motivation, whereas cognitive engagement has no significant effect, and this influence diminishes over time. Discussion and Conclusion: This study reveals the complex relationship between sports engagement and intrinsic motivation, delving into their dynamics in university education. The findings have key implications for optimizing sports education and student development. To improve learning and motivation, strategies should foster intrinsic motivation and enhance emotional engagement.