This study aims to examine how students' learning trajectories progress in an online social annotation environment, and how their cognitive processes and levels of interaction correlate with their learning outcomes. Three different types of activities (cognitive, metacognitive and social) were identified in the online environment. The time series of different levels of cognitive and metacognitive activities correlate with one another, indicating that a kind of symbiotic or ecological relationship exists among the cognitive and metacognitive processes. The multiple regression results show that low‐cognitive level activities mediate the effect of high‐cognitive level activities on student's performance in the group inquiry learning project. The results of multilevel analysis indicate that the average number of highlighted texts posted per person in a group accounted for over 50% of the variance of the group inquiry learning project scores. Further, the results also indicate that the level of collaboration within a group explains over 70% of the variance of the high‐level cognitive and metacognitive activities across different groups. In sum, group collaboration is found to be conducive to fostering high‐level cognitive and metacognitive activities.