Lack of parental care is one of the potential causes of bullying victimization of left-behind children (LBC) in China. In father-absent families, maternal involvement may be a protective factor against peer bullying, a topic that has been neglected in prior research. The current study examined the longitudinal influence of maternal involvement on father-absent LBC’s bullying victimization and the mediating roles of family functioning and children’s self-esteem. Three hundred and thirty-seven father-absent LBC in China participated in the current study at three-time points, and three hundred and eighty-six non left-behind children (NLBC) served as the comparison. The results indicated that: (1) a higher level of maternal involvement predicted less bullying victimization among father-absent LBC; (2) family functioning mediated the relationship between maternal involvement and father-absent LBC’s bullying victimization; (3) family functioning and self-esteem played a joint mediating role between maternal involvement and LBC’s bullying victimization; and (4) the mechanisms are different between father-absent LBC and NLBC. These findings highlight the essential role of the remaining parent in LBC’s bullying prevention.