Objective: To examine the association between academic stress and anxiety-depression comorbidity among college students and the potential moderating effect of physical activity, so as to provide a theoretical basis for the development of evidence based mental health promotion frameworks in higher education institutions. Methods: From October 2022 to June 2024, a total of 7 980 students from 21 universities across five provinces/municipalities in China, including Shanghai, Jiangsu, Zhejiang, Shandong, and Anhui, using a combination of convenience sampling and stratified random cluster sampling. Physical activity, academic stress, anxiety, and depression were assessed by using the 24 hour Movement Behaviors Questionnaire, the Chinese College Students Mental Health Screening Scale, the Generalized Anxiety Disorder-7, and the Center for Epidemiologic Studies Depression Scale, respectively. Binary Logistic regression was used to examine the associations between academic stress and anxiety, depression, and their comorbidity. The PROCESS macro was employed to test the moderating effect of physical activity. Results: The prevalence of anxiety-depression comorbidity among college students was relatively high (11.53%), with significant differences observed across grades and body mass index (BMI) categories ( χ 2=70.30, 24.63, both P <0.01). Binary Logistic regression revealed that, compared with low academic stress, moderate academic stress among male students was significantly associated with greater odds of anxiety ( OR =2.78), depression ( OR =2.75), and anxiety-depression comorbidity ( OR =2.89) (all P <0.01). High academic stress was associated with elevated odds of anxiety ( OR =6.66), depression ( OR =12.81), and anxiety-depression comorbidity ( OR =13.65) (all P <0.01). Among female students, moderate academic stress was associated with anxiety ( OR =2.58), depression ( OR =1.52), and anxiety-depression comorbidity ( OR =1.70) (all P <0.01). High academic stress increased the risk of anxiety ( OR =6.77), depression ( OR =6.81), and anxiety-depression comorbidity ( OR =7.48) (all P <0.05). The moderation analysis indicated that the interaction between total physical activity duration and academic stress had a significant netative moderating effect on anxiety-depression comorbidity among college students ( β =-0.03, P <0.01). Conclusions Academic stress increases the risk of anxiety, depression, and anxiety-depression comorbidity among college students. Physical activity may attenuate the adverse effects of academic stress on anxiety-depression comorbidity.