Background Externalizing behavior problems (EBP) is being increasingly viewed as a public health problem. Few studies have addressed EBP in Chinese hui nationality left-behind children (LBC). The aims of this current study to explore the prevalence of EBP and its influencing factors among hui nationality LBC in rural areas of China.Methods A cross-sectional study was conducted among school students from the southern rural areas in Ningxia, China (2012–2013). The general self-made questionnaire, Egma Minnen av Bardndosnauppforstran (EMBU), Eysenck Personality Questionnaire (EPQ for Children), Piers-Harri Children's Self-concept Scale (PHCSS) and Achenbach's Child behavior Checklist (CBCL for parents) were used to investigate the related information. Descriptive analysis and logistic regressions were conducted.Results The prevalence of EBP in hui nationality LBC and non-left-behind children(non-LBC) were 12.01% (46/383) and 8.57% (49/572), respectively, and there was no significant difference between them (χ2 = 3.037, P = 0.081). Multivariate logistic regression analysis showed that low self-concept of behavioral (OR = 13.709), introversion (OR = 11.188) and intermediate personality (OR = 9.349) were risk factors for EBP of hui nationality LBC, while the intermediate type of mother refusal and denial (OR = 0.430) was their protective factor.Conclusions Our findings suggest that parental migration is a risk factor for EBP among hui nationality LBC in rural China. And measures should be taken from self-concept development, personality development, and family education for the prevention of EBP of hui nationality LBC in rural areas of China.