The “conceptual graph” is a conventionally adopted assisted teaching method. Conceptual graphs display the achievements of students. This study proposes a novel learning activity called “Two-Phase Cooperative Learning.” The framework of this activity is based on the conceptual graph. The system includes the Dynamic Remedial Instruction Path (DRIP) and the grouping of cooperative learning phases. In phase 1, the DRIP is established and used to analyze the student knowledge structure for self-learning. In phase 2, a grouping cooperative learning subsystem is designed with the help of partners for advanced learning. The DRIP is composed of systematically guided study activities developed according to the learning status of individual students, and the established Remedial-Instruction Decisive Path (RID path) is used to identify the real misconceptions of students. Study results are kept in the knowledge structure. Phase 2 involves cooperative learning, which uses knowledge structures as a grouping strategy. This study calculates the assistant ability of each student, which represents a homogeneous and complementary relationship. The grouping goal of cooperative learning is based on the heterogeneous knowledge structure. This study adopted two-phase cooperative learning in two courses. The learning evaluation yielded positive experimental results. The evaluation shows that the cooperative learning activities were effective for student learning.