In recent years, the BOT financing mode becomes a popular international infrastructure financing model. It makes a full use of the foreign capital and private capital, and also makes a contribution to solve problems of financial shortage in the construction of infrastructure. It will also help the universities to go through the capital shortage when using the BOT financing mode into the construction of infrastructure. However, there are also imperfections in the qualitative and quantitative analyses of risk assessment by using this model. The author made a deep research on the application of the BOT financing model in the infrastructure construction of universities, and analyzed its risk by using a new kind of the AHP, which avoiding the disadvantage of the traditional AHP in some extent.