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Abstract This study aims to further understand the changes in physical activity level(PAL) and mental health among adolescents before and after the outbreak of COVID-19 and explore the protective role of physical activity (PA) on the mental health of adolescents during major disasters. A convenient sampling method was used to conduct a cross-sectional survey. The cross-sectional data from 2838 Chinese middle school students (mean age = 14.91 ± 1.71 years, 49.54% female) were used, of which 1,471 and 1,367 were in 2021 and 2022, respectively. The PAL was collected using the Physical Activity Questionnaire for Children (PAQ-CN), mental health status was collected using the Mental Health Inventory of Middle School Students (MMHI-60), sociodemographic information was collected using a self-reported questionnaire. Before and after the outbreak of COVID-19, the PAL of adolescents was 2.36 ± 0.74 and 2.50 ± 0.66, respectively, with a significant difference (p < 0.01, 95% CI: 0.09, 0.19). The mental health scores were 1.71 ± 0.60 and 1.86 ± 0.73, respectively, with a significant difference (p < 0.01, 95% CI: − 0.20, − 0.10). The detection rates of mental health problems were 27.50% and 35.50%, respectively. The rates of achieving PAL standards were 30.20% and 18.00% among adolescents, while the rates of not achieving PAL standards were 39.60% and 18.00%. PA is a protective factor for the mental health of adolescents during major disasters.