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Objectives To analyse changes in the prevalence of suspected scoliosis among children and adolescents in Heqing County, South-West China, over different periods and to identify risk factors for its progression.Design A mixed-methods study, including a cross-sectional survey and longitudinal follow-up.Setting Single-centre study. An angle of torso rotation (ATR) ≥5° was defined as a positive screening result and progression was defined as an increase in ATR ≥2°.Participants In November 2021, 22 740 students aged 6–18 years were screened; in May 2023, 28 009 students aged 6–18 years were screened. A total of 350 students with suspected scoliosis identified in 2021 were enrolled for longitudinal follow-up.Results The prevalence of suspected scoliosis was 2.47% in 2021 (22 740 students) and 3.14% in 2023 (28 009 students). Among 4468 students screened in both years, 109 (2.44%) tested positive in 2021 and 124 (2.78%) in 2023. Prevalence was significantly higher in girls (2.92% in 2021; 4.36% in 2023) than in boys (2.01% in 2021; 1.94% in 2023) and higher in the 10–18 years age group (3.38% and 4.11%) than in the 6–10 years age group (0.59% and 0.83%; both p<0.001). From 2021 to 2023, overall prevalence, as well as prevalence among girls and the 10–18 years age group, increased significantly (all p<0.001), whereas no significant changes were observed in boys (p=0.71) or the 6–10 years age group (p=0.07). Of 329 students with suspected scoliosis in 2021 who completed follow-up in 2023, 35 (10.6%) showed progression. Progression was significantly associated with lower body mass index (BMI) and higher baseline ATR, with correlation coefficients of −0.112 and 0.127, respectively (both p<0.01). Binary logistic regression showed that higher BMI was associated with reduced progression risk (OR=0.827, 95% CI 0.700 to 0.978, p<0.05).Conclusion The prevalence of suspected scoliosis in children and adolescents in Heqing County was higher in 2023 than in 2021. Approximately 10.6% of individuals with suspected scoliosis progressed over 1.5 years. BMI may serve as a protective factor against scoliosis progression.