The purpose of this study is to investigate and compare students' collaborative inquiry learning behaviors and their behavior patterns in an augmented reality (AR) simulation system and a traditional 2D simulation system. Their inquiry and discussion processes were analyzed by content analysis and lag sequential analysis (LSA). Forty university students were divided into dyads and then randomly assigned into AR group and traditional 2D group to collaboratively conduct an inquiry task about elastic collision. The results of the content analysis and LSA indicated that both systems supported students' collaborative inquiry learning. Particularly, students showed high frequencies on higher-level inquiry behaviors, such as interpreting experimental data or making conclusions, when using these two simulations. By comparing the behavioral patterns, similarities and differences between the two groups were revealed. The AR simulation engaged the students more thoroughly in the inquiry process. Moreover, students in both groups adopted the same approaches to design experiments. Due to the line of AR research is in its initial stage, suggestions for future studies were proposed.