The development of students' practical operation and their collaborative problem solving (CPS) ability are emphasized in higher education nowadays. Providing students a simulation learning tool and an social networking environment can improve the students' learning in CPS activities. This can be a potential learning environment for the students when the automatic scaffolding guidance tools are appropriately given to them. Therefore, the present study developed a scaffolding-based CPS learning environment. This empirical study explored learners' learning performance. The students' online discussion messages were also encoded for the later quantitative content analysis to explore their cognitive process in CPS activities. The study included 94 participants, who were divided into the "study sheet group" (use the simulation tool and paper study sheets for discussions) and the "scaffolding mind tool group." The results showed that learning performance of the "scaffolding mind tool group" was significantly better than that of the "study sheet group." Moreover, learners in the "scaffolding mind tool group" showed more diverse levels in the cognitive process. The researcher further conducted a "Lag sequential analysis" based on the coding results. The results also suggested that the "scaffolding mind tool group" showed more diverse cognitive process transitions in their behavioral patterns.