Using data from China Education Panel Survey (CEPS), this study aims to investigate the association between perceived appearance, body shape and adolescent academic achievement, elucidate underlying mechanisms, and examine the heterogeneous relationships across different groups. The results suggest that there is an ugliness penalty rather than a beauty premium in Chinese middle school. Overweight and obese students have lower academic achievement than normal weight students. These findings remain robust after replacing the independent variable and dealing with selection bias. Mechanism analysis reveals that teacher preference and non-cognitive ability are important transmission mechanisms linking perceived appearance with academic achievement. Academic achievement disadvantage in obese students compared with normal weight students is partially transmitted through cognitive ability. Additionally, poor perceived appearance and obesity have a greater negative impact on the academic achievement of disadvantaged groups. These findings better our understanding of perceived appearance and body shape in the formation of educational stratification and provide a scientific basis for equalizing the educational process within schools.