Design protocol is the documentation of design behavior. Protocol analysis is a method for recording and analyzing design behaviors in the design process based on the theory of cognitive science. This study is to explore how to apply protocol analysis in the design process to understand the design thinking and the issues in documentation and analysis. This study plans and proceeds a case-based de sign experiment, explore various approaches in protocol analysis, and compares different design tools and behaviors. This study applies the retrospective protocol analysis and prepares five analytic tables for recording graphical data in the design process for analyzing the design thinking behaviors. The analytic framework and the result are presented.