As human-centered design has become new paradigm in the whole field of design, they make an effort to understand users in the field of graphic interface design. However, there are not much of study to systematic process for human-centered approach in graphic interface design. Therefore, in this paper, the study was conducted to develop application methodology of prototype in the graphic user interface design process. The study consists of three sections. first, definition, types and application methods are introduced by secondary research. Second, all the knowledge gathered above by secondary research are integrated in the newly proposed Prototype-based interface design process. There are many types of prototype from idea sketches on the paper to final working prototype realized by computer. It is needed to develop and test appropriate prototype with appropriate techniques by objectives of the stages. Finally, the proposed prototype-base design process is verified and exemplified through the process of using prototype in the development of multi-user educational multimedia product.