The aims of this study were to systematically evaluate and comparatively analyse the mental health status of left-behind children (LBC) in China and to provide a scientific basis for mental intervention and healthy education for LBC. Six electronic databases were searched for studies (published from 1 January 2010 to 5 March 2018) of the mental health of LBC using the Mental Health Test scale. We only selected original articles that either reported the incidence of serious mental health status or the means and standard deviations of each factor score of the scale. The pooled rates and weighted mean difference were calculated. The results indicated that the incidence of serious mental health status of LBC is nearly 2.7 times higher than that of non-LBC. The scores for most of the factors analysed by the Mental Health Test of LBC were higher than those of non-LBC. In addition, the mental health status of left-behind girls is worse than that of left-behind boys. Except for impulsive tendency, there was no significant difference in the mental health status of LBC in primary and junior high schools. In terms of the different types of guardianship, the mental health status of LBC under a grandparent's guardianship and parental peer' guardianship is more serious than that of LBC under a single-parent guardianship. The mental health status of LBC is poor, particularly for left-behind girls. The primary mental problems faced by LBC are learning anxiety, social anxiety and physical symptoms. It is necessary to develop more targeted measures to prevent and manage LBC.