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Abstract Background The major public health crisis caused by the rapid spread of the coronavirus disease 2019 (COVID-19) and the large-scale public health measures such as social isolation and school closures enforced by some countries have severely affected on the physical and mental wellbeing of children and adolescents globally. This study aimed to estimate the prevalence of the psychological impact and investigate the similarities and differences in the influential factors for generalized anxiety disorder among rural adolescents as a relatively lesser noticed population the outbreak of COVID-19. Methods From May 11 to 22, 2020, a total of 1,179 adolescents, including Grade 5–6 in primary school and Grade 7–8 in middle school, were selected by multistage sampling in three Southern Chinese cities (Shantou, Guangdong Province; Hezhou, Guangxi Province; Nanchong, Sichuan Province), and completed the questionnaires including sociodemographic, generalized anxiety disorder, academic stress, coronaphobia, knowledge of COVID-19, and precautionary measures. ANOVA, Chi-square test, Kruskalwallis H test and multivariate linear regression were performed in the statistical analysis. Results The average scores of generalized anxiety disorder during the past two weeks were 3.43 (SD 4.46), 4.47 (SD 5.15), and 4.10 (SD 4.94) in Shantou, Hezhou and Nanchong, respectively. For the pooled data, academic stress (P |