Interpersonal physiological synchrony has been consistently found during collaborative tasks. However, few studies have applied synchrony to predict collaborative learning quality in real classroom. To explore the relationship between interpersonal physiological synchrony and collaborative learning activities, this study collected electrodermal activity and heart rate during naturalistic class sessions and compared the physiological synchrony between independent task and group discussion task. The students were recruited from a renowned university in China. Since each student learn differently and not everyone prefers collaborative learning, (...) participants were sorted into collaboration and independent dyads based on their collaborative behaviors before data analysis. The result showed that, during group discussions, high collaboration pairs produced significantly higher synchrony than low collaboration dyads. Given the equivalent engagement level during independent and collaborative tasks, the difference of physiological synchrony between high and low collaboration dyads was triggered by collaboration quality. Building upon this result, the classification analysis was conducted, indicating that EDA synchrony can identify different levels of collaboration quality. (shrink)