Currently, China’s low-income housing supply is more and more enlarged, low-income housing types are continuously innovated, the benefited Chinese are diversified, as a result, the management system for low-income housing should be perfected in all parts of China, the low-income housing supply and management should consider the multivariate and multi-level characteristics of the group who need the apartments, the entrance and withdrawing requirement for low-income housing should be constantly adjusted. The low-income housing management in Chongqing has the problems in short of necessary legal support, incomplete management departments, weak related agencies, incomplete duty of the related agencies, simple supply method, big gap between standard rents and the expected rents in middle and low income group, unfair ensuring policies because of the enlargement of low-income group, incomplete entrance and approval method, and difficult withdrawing supervision. Chongqing should make related laws and regulations as soon as possible, perfect governmental duty, build low-income housing management system with clear division of labor and with distinct management levels, use multivariate supply method, set rents according to affordable ability of low-income group to realize scientifically reasonable management and supply of low-income housing, rationally determine supply range for low-income housing, strictly conduct low-income housing affairs, carry out effective withdrawing management to ensure demand management for low-income housing.