In this study, a collaborative problem solving-based STEM course was implemented in a seventh-grade class. This study aimed to examine the effects of students' prior knowledge on their CPS-based STEM learning processes by using a mixed-methods approach. First, a lag sequential analysis was used to investigate individual cognitive and metacognitive behaviors of students with different prior knowledge levels, while a dialogue analysis was used to explore their social behaviors during discussion. The results indicated that students with sufficient prior knowledge conducted cognitive and metacognitive strategies more effectively during individual thinking. On the contrary, students who lack prior knowledge focused more on social strategy and engaged in cognitive strategies through group contributions. The dialogue analysis revealed different social interaction patterns that were affected by using CPS skills, cognitive tools, and the group dynamics. Second, interviews were conducted and analyzed to provide rational explanations for students' learning behaviors and further investigate the effects of their prior knowledge. Finally, specific instructional designs are provided to bridge the gap between high and low prior knowledge students.