Parental migration has been an important predictor of left-behind children’s developmental outcomes. Based on the ecological model of rural left-behind children’s development, we systematically reviewed studies related to rural left-behind children’s mental health in China and investigated left-behind children’s mental health and its influencing factors. Thirty-two studies involving 28,629 participants met the inclusion criteria were included in our meta-analysis to compare mental health of left-behind children and non-left-behind children. Twenty-two studies involving 8,634 participants were included in gender difference meta-analysis. The results indicated that left-behind children report more mental health problems than non-left-behind children, left-behind girls were confronted with higher level of mental health problems than left-behind boys, left-behind children in primary school and junior high school reported more mental health problems than those in senior high school, and self-guardian children have more serious mental health problems than children guarded by grandparents, former generation, and single parent. Implications for future practice were analyzed from family, school, and government perspectives.