Mathematics is closely related to daily life. However, it is one of the subjects causing anxiety during the learning process for the primary school students. The courses conducted by using the game-based learning (GBL) model can enhance the learners' willingness to learn as well as learning interest. Therefore, this study adopts the input-process-outcome GBL model to develop mathematics learning system with diagnostic learning in primary school mathematics course. In addition to the exploration on the impact of different teaching methods on learning performance, according to the research results, using GBL system in learning is better than the traditional learning by paper-based while the teaching with diagnostic mechanism is even better than the general GBL system. Moreover, it can enhance learning motivation and learning achievement.