Objective To study the life quality status of left-behind children and its influencing factors by a sampling survey comparing with the non-left-behind children in Chongqing, so as to provide a basis for improving children's quality of life. Methods We adopted a multistage cluster sampling and conducted surveys by home visiting; the children's quality of life was assessed with Chinese version of PedsQL4.0 children's quality of life measuring scale. The life quality status of left-behind and non-left-behind children was evaluated by their scale scores, and the factors influencing children's quality of life were analyzed by multiple-factor analysis. Results The scores of total score of life quality, physiological function, emotional function, social function, and role (performance in school) function of left-behind children in Chongqing were 82.50±11.56, 87.03±13.58, 77.55±16.05, 85.64±14.85, and 77.05±14.22, respectively; and the scores for un-left-behind children were 86.72±10.12, 89.96±11.67, 83.26±14.65, 90.66±12.44, and 81.08±13.67, respectively. The total score and scores of each dimension of left-behind children were all significantly lower than those of non-left-behind children (P<0.01). Multiple linear regression analysis found that the left-behind status, age, and per capita expenditure of a family were the main factors influencing the children's quality of life, with the left-behind status having the greatest influence; moreover, the left-behind status could greatly influence the emotional function, social function and role function. Conclusion To reduce "left-behind" phenomenon is a direct method to improve children's quality of life and increase their physical and psychological health. When "left-behind" phenomenon can not be completely eliminated, families, schools and society should pay more attention to left-behind children, making joint efforts to protect the physical and psychological health of left-behind children.