ObjectivesPrevious studies have used latent profile analysis (LPA) to examine rural left-behind children’s anxiety. Further study is needed to identify the heterogeneous characteristics of rural left-behind children’s anxiety and explore the related factors.SettingA cross-sectional survey using a school-based sample was conducted in January 2018 in Qingxin district, Qingyuan city, Guangdong province.Participants1026 left-behind children (effective response rate of the questionnaire: 95.39%).Main outcome measuresProfile latent classes (LC) and anxiety disorder.ResultsThe LPA identified three anxiety LC: ‘low anxiety’ (56.6%), ‘medium anxiety’ (34.8%) and ‘severe anxiety’ (8.6%). The multinomial logistic regression model was used to predict the relationship between personal, family, school factors and anxiety. We found that the variables directly related to lower anxiety classes included age (12–14 years), harmonious or fair relationship with classmates, no neglect, harmonious parental relationship and the duration of mother migration <6 months.ConclusionsThese findings suggested the need for careful consideration of differences in anxieties among rural left-behind children. Identifying latent subgroups may provide an empirical basis for teachers and public health practitioners to implement anxiety intervention efforts.