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This mixed-method study examined the impact of virtual and physical presence on the simulation-based learning process and outcome. A virtual-reality (VR), embodiment integrated learning environment is constructed to provide simulation-based teaching training to university teaching assistants (TAs). A total of 42 chemistry TAs were randomly assigned to a hybrid-presence group and a physical-presence-only group. In both groups they practiced targeted teaching skills by coaching a simulated class, laboratory, and help session during a 3-hour training session. The study found a significant improvement in TAs’ teaching knowledge after the training session. The physical presence, in comparison with the mixture of physical and virtual presence, better support collaborative role-playing and learning outcome in the synchronous co-located setting.