In recent years, many people have devoted their efforts to the issue of quality of Web site. The concept of quality is consisting of many criteria: quality of service perspective, a user perspective, a content perspective or indeed a usability perspective. This research conducts some tests to measure the quality of Malaysian University website via web diagnostic tools online. We propose a methodology for determining and evaluating the best Malaysian university website based on many criteria of website quality, consists of Linear Weightage Model, Analytical Hierarchy Process, Fuzzy Analytical Hierarchy Process, and one new hybrid model. This new hybrid model has been implemented using Fuzzy Analytical Hierarchy Process (AHP) and linear weightage model to generate the weights for the criteria which are much better and guarantee more fairly preference of criteria. The result of this study confirmed most of Malaysian University websites are neglecting the performance and quality criteria. By applying Hybrid model between FAHP and LWM approach for website evaluation has resulted in significant acceleration of implementation, raised the overall effectiveness with respect to the underlying methodology and ultimately enabled more efficient and significantly equal or better procedure compared with other methods. © 2010 IEEE.