In Taiwan, when students learn in experiment-related courses, they are often grouped into several teams. The familiar method of grouping learning is "Cooperative Learning". A well-organized grouping strategy improves cooperative learning and increases the number of activities. This study proposes a novel pedagogical method by adopting the Learning Diagnosis Diagram to obtain students' knowledge structure. According to each knowledge structure of the student, this study proposes dynamic grouping to solve problems in the conventional once-and-for-all grouping strategy. The dynamic grouping method achieves the best complementary groups for further learning stages. Two courses were applied to conduct the proposed Two-phase Cooperative Learning. Complementary grouping methods and more interaction among team members are helpful for increasing the effect of learning. Evaluation results indicate that the proposed method significantly improves the learning achievement of all learners. (Contains 6 figures and 5 tables.)