The post-earthquake reconstruction of damaged cities and towns requires reasonable site selection and safety assessment. Site selection task involves complex factors such as earthquake fault, geologic hazard, site stability, national well-being and the people's livelihood, and economic development and sustainability. It is a task of complicated engineering system. Problem considerations can follow these basic principles: (a) to the towns which located at the earthquake fault zones and deterioration on geological environment and had severe hidden danger of geologic hazard, they must be removed to other places; (b) to the towns which was damaged, but is far away from the earthquake fault zones and does not exist geologic hazard, they should be in-situ reconstructed and the reconstruction should be carried out according to principles of science planning, avoidance norms, reasonable adjustment to the aseismicity standards. On the process of the post-earthquake reconstruction, attentions should be paid to the disguised geologic hazards, multiplicity of induced factors and long-term sustainability and to strengthen suitability evaluation on geological environment and risk assessment on geologic hazard. Based on the post-earthquake actual survey, this paper assesses the problems of site selections on the reconstruction of Beichuan town, Qingchuan town and Muyu town of Qingchuan County. Based on the evaluation of site engineering geology and geological environment, the paper gives some typical suggestions for the site selection on reconstruction of the towns.