Abstract: Pen-based user interface (PUI) is a primary style in the post-WIMP world, which has many potential advantages such as naturalness and being easy to use and to learn. However, the application-centered software design method cannot ensure the pen-based user interface to keep these advantages when pen-based interactive system is developed. Hence, a software design communication model is first analyzed. Then, based on this model, a user-centered software design method is presented, which is described in detail through the scientific diving training management system. The evaluations of the practical systems show that the method can effectively improve the usability of pen-based interactive systems.