With the increasing transfer of rural labor, the problems of the left-behind children attract extensive attention. This paper is based on a large sample random survey in Jiangxi Province and Anhui Province’s primary and high school in China, researching students and their guardians, head teachers, headmasters. The research applied a combination of quantitative and qualitative methods to study on the effect of parents’ migrant working on the education of the rural left-behind children in details. The study found that the effect changes with learning stages and subjects. The supervision of parents and teachers is helpful to the left-behind children at primary school stage, while it cannot show significant help to those at junior high school stage, which may even have the opposite effect. The number of siblings and living on campus do not have a negative effect on children’s study, which even have a positive effect in some respects. Children’s own prospect of their education have a significant positive effect on their learning performance, while parents’ prospect only have a positive effect on learning performance of the left-behind children at junior high school stage.