It is well known that the web design is composed of several factors which are interacting with each other. However, the current approach to web design had been focused on modifying specific factors without considering its impact on other factors. In this sense, we propose more holistic approach to the web design by using fuzzy cognitive map. For this purpose, we form an illustrative fuzzy cognitive map for the web design which is based on the literature, and analyzed and impact of change in a specific factor on other factors. Especially, to improve the output analyzability, we suggested an advanced version of fuzzy cognitive map called stratified fuzzy cognitive map. After simulating the fuzzy cognitive map for web design, we could conclude that our approach is robust and effective compared to the traditional web design approach.