BACKGROUND: There has been an increasing prevalence of parental separation in China due to divorce or migration for work in recent decades. However, few studies have compared the impacts of these two types of separation on children's mental health. This study aimed to investigate how parental divorce and parental migration impact children's mental health and self-injurious thoughts and behaviors (SITB), while considering positive factors, including parent-adolescent communication and psychological resilience. METHODS: We randomly recruited participants in grades 5-8 from 18 schools in 2 counties in Anhui Province. A self-administered questionnaire was conducted to measure children's mental health, SITB, parent-adolescent communication, psychological resilience, and socio-demographic characteristics. RESULTS: Data from 1026 children with both parents migrating (BLBC), 1322 children with one parent migrating (SLBC), 475 children living in a divorced family (DC) and 1160 children with non-migrating parents (NLBC) were included. Regression model results showed that, compared to the other three groups (BLBC, SLBC, NLBC), DC exhibited higher internalizing problems (p < 0.05), higher externalizing problems (p < 0.01), less prosocial behaviors (p < 0.05), and higher rates of suicidal ideation (SI) (p < 0.05) and non-suicidal self-injury (NSSI) behaviors (p < 0.05) when adjusting for social-demographic variables. However, when further adjusting for parent-adolescent communication and psychological resilience, DC no longer had higher levels of internalizing problems, externalizing problems, NSSI and SI than left-behind groups (BLBC, SLBC). CONCLUSIONS: The experience of separation from divorced parents had stronger negative effects on the mental health of children than was observed in LBC. The Chinese government should design special policy frameworks that provide support to DC.