Background: Direct exposure to public health emergencies is associated with increased mental disorders. It is less clear about the prevalence of common mental disorders and its correlates in Chinese adolescents after experiencing public health emergencies. Objective: This longitudinal study aims to estimate the prevalence of common mental disorders (i.e. depression, anxiety, and post-traumatic stress disorder) and its correlates in a sample of Chinese adolescents after experience a public health emergency, namely the novel coronavirus disease 2019 (COVID-19). Method: This study intends to recruit 3,428 Chinese adolescent students from high and middle schools in the baseline survey. This study will track these recruited participants every 6 months via three-wave follow-up (i.e. 6-month, 12-month, and 18-month follow-ups). The demographics (e.g. age, gender, education, family background, and residence) and psychosocial factors (i.e. exposure to traumatic events, religious belief, social media exposure, loneliness, and perceived social support) associated with common mental disorders (i.e. depression, anxiety, and post-traumatic stress disorder) will be investigated in this sample population. Furthermore, a hardcopy self-report questionnaire will be disturbed to all participants. Additionally, the cross-sectional analyses will be first conducted to estimate the prevalence of mental disorders and their correlates in data of baseline survey. After obtaining the longitudinal data, the relative risk, incident rate ratios, latent class analysis, and structural equation model may be performed in this study. Missing data will be solved by the multiple imputations. Data analysis tools included the Stata 16.0 and Mplus 8.4. Discussion: This longitudinal study will better help to understand the prevalence changes of mental disorders among Chinese adolescents following the COVID-19. These findings have the potential to provide empirical evidence about the burden of mental disease and key drivers of Chinese adolescents following the COVID-19, which can benefit the formation of public policy and mental health intervention programming. This study will close the gaps that a lack of epidemiological studies about the mental disorder prevalence and related risk factors.