Objective To investigate the prevalence status of dental caries status amongleft-behind school-age children aged in rural northern Guangxi, and carry out targeted prevention and early intervention accordingly. Methods A total of 818 rural school-age children in rural areas of Lingui District, Guilin City, Guangxi were selected as study subjects, including 409 left-behind children (left-behind group) and 409 non-left-behind children (non-left-behind group). The oral health status (caries prevalence of deciduous and permanent teeth and teeth restoration rate) was compared between the two groups. The left-behind group was then divided into a caries-affected group and a caries-free group according to caries status. A multivariate logistic regression model was used to analyze the influencing factors of dental caries among left-behind children. Health promotion and intervention measures (pit and fissure sealing, atraumatic restorative treatment) were implemented based on the analysis results, and the intervention effect was observed. Results The left-behind group exhibited a lower teeth restoration rate, along with higher mean deciduous teeth caries and mean total caries score, compared with the non-left-behind group (P<0.05). Multivariate logistic regression analysis identified gender, fluoride toothpaste use, regular fluoride application, history of orthodontic treatment, and awareness of cariogenic foods as influencing factors associated with dental caries in left-behind children (P<0.05). After the intervention, left-behind children demonstrated decreased deciduous teeth caries prevalence rate and total caries prevalence rate, reduced mean deciduous teeth caries and mean total caries scores, and improved awareness of the benefits of pit and fissure sealing relative to baseline (P<0.05). Conclusion Compared with non-left-behind children, left-behind children in rural northern Guangxi had a higher mean total caries score. Gender, fluoride toothpaste use, regular fluoride application, history of orthodontic treatment, and awareness of cariogenic foods are the influencing factors for dental caries in left-behind children. Targeted interventions based on these influencing factors can reduce the caries prevalence of left-behind children and improve their oral health knowledge.