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In this study, we explored the relationships among students’ perceived challenges in collaborative learning, emotion regulation strategies (ie, reappraisal and suppression), and emotion synchrony (ie, valence synchrony and arousal synchrony) in natural classroom settings. We performed the partial least squares structural equation modeling (PLS-SEM) method for data analysis. The results revealed a positive and direct effect of cognitive reappraisal on arousal synchrony, and a negative and direct effect of cognitive reappraisal on valence synchrony. Moreover, students’ perceived challenges in collaborative learning had a negative effect on their arousal synchrony. Students’ perceived challenges also played a mediating role in the relationship between cognitive reappraisal and arousal synchrony. As a total effect, cognitive reappraisal still positively and significantly predicted arousal synchrony. This study provided insights into students’ emotional responses in collaborative learning and informed the design of collaborative learning environments. This study has also methodological implications regarding the analysis of emotion synchrony.