Using propensity score matching method, this study examined the effect of boarding on campus on left-behind children (LBC)'s sense of school belonging and their academic achievement. The condition of boarding schools was also examined closely in this study. Data were collected from 6,638 students from 74 rural boarding schools in 11 provinces in western China. Results indicated that boarding on campus had a negative effect on LBC's sense of school belonging as well as their academic achievement. Specifically, left behind boys who live on campus had a lower level of school belonging than those left behind girls. The academic achievement of LBC in primary school was more easily influenced than that of junior middle school students in a negative way, as well as their sense of school belonging. What is more, LBC in boarding schools were negatively influenced by the low quality of boarding schools such as facilities, management, and life. This finding suggests that policies regarding using boarding school to solve the problem faced by LBC should be reconsidered, and the condition of boarding schools should be improved by improving boarding facilities, management, and life for boarding children, and reducing the number of male and primary school LBC attending boarding schools.