In China, there are an estimated 41 million left-behind children (LBC). The objective of this study was to examine the mental health of current-left-behind children (current-LBC) and previous-left-behind children (previous-LBC) as compared to never-left-behind children (never-LBC), while considering factors like parent-child communication. Children were recruited from schools in rural areas of Anhui province in eastern China. Participants completed a questionnaire focusing on migration status, mental health, and parent-child communication, measured with the validated Strengths and Difficulties Questionnaire (SDQ) and Parent-Adolescent Communication Scale (PACS). Full data were available for 1251 current-, 473 previous-, and 268 never-LBC in Anhui province. After adjusting for all confounding variables, the results showed that both current and previous parental migration was associated with significantly higher mental health difficulties, including aspects of emotional symptoms, conduct problems, hyperactivity, and total difficulties. Additionally, we found that difficulties communicating with parents were strongly associated with the presence of greater total difficulties in children. Parental migration has an independent, long-lasting negative effect on children. Poor parent-child communication is strongly associated with children's mental health. These results indicate that parent-child communication is important for the development of children, and interventions are needed to improve migrant parents' understanding and communication skills with their children.