One hundred and thirty three quake lakes were formed in Wenchuan Earthquake of May 12. There may be several or even a dozen quake lakes in the same drainage basin. During the emergency treatment of quake lakes, due to constraints of resources and time, it is often imperative to select one or a few quake lakes of high priority in the same drainage basin for treatment in order for the entire drainage basin to safely pass the flood season. There are many factors involved in the optimization of emergency treatment project of quake lakes and these factors are usually of different nature. This article proposes to use a multi-level, multi-factor optimization method in decision making of emergency treatment of quake lakes based on the concept and operation properties of fuzzy-consistent matrix. This method is convenient and practical when many qualitative factors are involved and the determination of membership function is difficult. A case study was conducted for the 16 quake lakes on the Mianyuan River by using the proposed method. Three quake lakes selected according to case study results went through emergency treatment before the 2009 flood season, helping the entire Mianyuan River safely pass the 2009 flood season.