Objective To investigate the status and influencing factors of the quality of life (QOL) on adolescent migrant students in an urban area of Chongqing. Methods A total of 3,512 students (1,821 boys, 1,691 girls) aged 9 to 16 from an urban district of Chongqing were enrolled with random stratified and cluster sampling method. General situation, QOL, depression and pubertal timing of the populations were studied. Results The score of QOL and that in physiology and society in migrant students were lower than those in non-migrant students (P < 0.05). Multivariate logistic regression analysis showed that high learning stage, depression and early puberty were the risk factors of QOL; good family economic condition and relation were the protective factors of QOL. High education level of father was the protective factor of QOL of adolescent migrant girls; high education level of mother was the protective factor of QOL of adolescent migrant boys (P < 0.05). Conclusions The QOL of migrant students is lower than that of nonmigrant students. Learning stage, family economic condition, family relation, education level of parent, depression condition and timing of puberty are the influence factors of QOL of adolescent migrant students. Paying attention to adolescent migrant students' family living environment, psychology and puberty development can effectively improve their QOL.