Since a course management system consists of the tools which faculty and students are repeatedly using the same function, it should be designed by a particular methodology to avoid users from unnecessary operations. To conduct a quantitative analysis for the user interface of the Web based course management system, we defined mouse operation as a criterion factor and developed a tool to trace the mouse movement on the PC display. This paper proposes how to improve the user interface in perspective from the optimization of process, selection of design components to form the user interface, and its layout. Finally the quantitative result is shown to apply this idea for designing the user interface.