After referring and designing the evaluation system, the author uses an improved AHP, expert investigation and integrated analysis and other methods to evaluate their library website of the following universities in Nanjing: Nanjing Agricultural University, Nanjing University of Science and Technology and Nanjing University of Aeronautics and Astronautics, including comparative analysis of three general merits of University Library Web site level, their characteristics and the drawback, and provides reference recommendations to university libraries website.