The present study aims to investigate the impacts of father-child communication on the mental health of left-behind children (LBC), and the role of maternal migration and mother-child communication in this correlations. A cross-sectional study was conducted in Anhui, China, from April 2018 to March 2019. Among 5253 valid responses, 1599 LBC who self-reported that their fathers were migrants at the time of the survey were included in the present study. There are three major findings: first, maternal migration can negatively influence LBC’s father-child communication frequency and quality; second, both higher father-child communication frequency and quality can promote LBC’s mental health; third, mother-child communication can enhance the protective effects of father-child communication quality on LBC’s mental health. Thus, we propose that, to promote the mental health of children with both parents migrating, it is of great importance for mothers and fathers to realize that direct father-child communication matters. And more direct father-child communication should be encouraged for children with both parents migrating.