Objective: To investigate the association of sleep and circadian rhythm disruption indicators (including chronotype, sleep duration, and social jetlag) with co-occurring depressive and anxiety symptoms among primary and secondary school students, so as to provide a reference for promoting their mental health. Methods: In October 2023, a total of 15 944 primary and secondary school students were recruited from Nanjing, using a stratified cluster random sampling method. The Morning and Evening Questionnaire-5, Center for Epidemiological Studies Depression, and Generalized Anxiety Disorder-7 were used for the survey. Chi-square test was employed for intergroup comparisons, and Logistic regression model was applied to analyze the independent and joint effects of sleep related factors on comorbid symptoms of depressive and anxiety among primary and middle school students. Results: The prevalence of co-occurring depressive and anxiety symptoms among primary and secondary school students in Nanjing was 16.9%. After adjusting for covariates, Logistic regression analysis revealed significant independent associations between evening chronotype ( OR=6.55, 95%CI =5.59-7.68), insufficient sleep duration ( OR=3.05, 95%CI =2.60-3.59), and social jetlag ≥2 h ( OR= 2.09 , 95%CI =1.85-2.37) with comorbid symptoms of depressive and anxiety among students (all P <0.05). Concurrent of evening chronotype and insufficient sleep ( OR=7.54, 95%CI =3.55-16.01), as well as evening chronotype and social jetlag ≥2 h ( OR=4.18, 95%CI =3.01-5.81), were associated with an increased risk of co-occurring depressive and anxiety symptoms (both P < 0.05 ). In the female and high school student subgroups, the combination of evening chronotype and insufficient sleep or social jetlag ≥2 h showed stronger joint effects on co-occurring depressive and anxiety symptoms [ OR (95% CI )=8.46(3.25-22.04) and 15.90(3.66-69.08); 7.87(4.90-12.65) and 4.85(3.10-7.59), respectively; all P <0.05]. Conclusions Evening chronotype, insufficient sleep, and social jetlag≥2 h may serve as risk factors for comorbid symptoms of depressive and anxiety in school aged populations. Paying attention to the coexistence of multiple sleep related risk factors may help mitigate the occurrence of emotional disorders in this demographic.