The comfortable housing project for low-income urban residents possess many special characteristics such as large numbers, dispersed distribution, the large-scale of construction, urgent time schedule and strict requirement of high quality. To ensure reasonable period and construction cost, it is also necessary to reform and innovate the way of construction management thinking and working methods. Pre-control measures of construction quality are put with emphasis on transforming passivity supervision into initiative forewarning. Management efficiency of the comfortable housing project can be enhanced. The comfortable housing project for low-income urban residents is built into environmental project taken to develop energy-saving and ground-saving residential in our country. It is a realistic and sharp contradiction that construction enterprises are pursuing profit when indemnificatory housing constructing is weak of profit, and that it is an easily occurred problem that the quality of indemnificatory housing is not security. In this paper, based on the six sigma quality management the Quality Assurance System of indemnificatory housing is put forward, which can be regarded as guidance for construction enterprises.