Objective: To investigate the relationship between different physical activity pattern and trajectories of anxiety and depression scores in college students, and to provide evidence for exploring the influence of physical activity on the development of anxiety and depression. Methods: A total of 1 265 college students from grade 2017 in a comprehensive university were investigated longitudinally for five times through stratified cluster sampling. Physical Activity Rank Scale-3(PARS-3), Self-rating Anxiety Scale(SAS), and Self-rating Depression Scale(SDS) were used, and latent class linear mixed models(LCLMM) were used to identify the trajectories of anxiety and depression scores and multinomial Logistic regression models were used for exploring the relationship between small persistent status of physical activity among the five surveys and subgroups of trajectory and anxiety and depression scores. Results: A total of 940(74.3%) college students were indentified as low persistent physical activity group and 325(25.7%) of them were identified as moderatre-to-high persistent physical activity group. The trajectories of anxiety score were classified into three groups:low level group, high level-decreasing group, and high level group. The number and proportion of the three groups were 686(54.2%), 144(11.4%), 435(34.4%), respectively. The trajectories of depression score were classified into four groups:low level group, moderate level-decreasing group, moderate level-increasing group, and high level group. The number and proportion of the five groups were 604(47.8%), 170(13.4%), 177(14.0%), 314(24.8%), respectively. Compared to the students with moderate-to-high persistent physical activity, higher persistent physical activity was associated with higher risk of keeping anxiety score at a high level(OR=1.78), and higher odds of decreasing depression score at moderate level(OR=0.67), as well as with higher risk of increasing depression score from a moderate level(OR=1.79), and increase the risk of keeping depression score at a high level(OR=1.97)(P<0.05). Conclusion Low persistent physical activity of college students could increase the risk of anxiety and depression at a high level. Relevant departments in universities should encourage students to take part in physical activity,with special focus given to individuals with less amount of physical activity and take effective interventional measures to modify the development of anxiety and depression.