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Background: Collaborative computer simulations are available on some online platforms which support students at distributed locations to synchronously collaborate on the simulations to learn sciences. However, how students collaborate with each other in collaborative simulations is not clear. Objectives: The aim of this study was to investigate whether functional interdependency would influence learning. Methods: Two collaborative learning models with different functional interdependencies were examined (the synchronous model and the distributed accountability model). Multiple data sources obtained from 64 students were collected and analyzed. We discuss the collaborative learning with two levels of factors: the individual‐level factors (i.e., individual perceptions of teamwork quality, visual attention and learning performance before and after a simulation activity) and the pair‐level factors (i.e., discourse data and joint attention). Given that the pair‐level factors in the collaborative learning environment may affect the individual‐level factors, we further discuss the interactions of the two levels of factors in different collaborative learning models with hierarchical linear modeling (HLM) analysis. Results and Conclusions: The analytical results of the individual‐level factors found participants in the distributed accountability model demonstrated more frequent and longer attention to the learning activity. Furthermore, the results indicated that the two simulation learning activities would enhance the participants' learning performance except in Q2. For the pair‐level factors, the results demonstrated that the participants in the distributed accountability model showed more active discourse segments but similar joint attention patterns in the learning activity. The results of the HLM analysis indicated that the students in the distributed accountability model had to collaborate with their partners through more constructive dialogue, and focused on the same areas of interest to enhance their learning performance, as the complexity of the distributed accountability design was implemented in a simulation learning activity. Major takeaways: We found that the increase of functional interdependency cannot guarantee students' learning effect in collaborative learning and may hinder the communication that is needed during collaboration. Researcher may need to consider other collaboration tools to enhance the reciprocal reflection. Lay Description: What is already known about this topic: Collaborative simulations are helpful in making the learning process cohesive.The learning effects of functional interdependence in collaborative learning are under debate. What this paper adds: We examined collaborative learning models with different functional interdependencies.We discuss the collaborative learning with the individual‐, the pair‐level factors and their interactions Implications for practice and/or policy: The importance of decreasing cognitive load induced by simulation with high functional interdependency.It is necessary to increase participants' transactive and constructive engagement in collaborative models. [ABSTRACT FROM AUTHOR]