Emotions play a crucial role in the learning process, yet there is a scarcity of studies examining emotion dynamics in problem-solving with fine-grained data and advanced tools. This study addresses this gap by investigating the emotional trajectories during self-regulated learning (SRL) phases (i.e., forethought, performance, and self-reflection) among 47 medical students utilizing an intelligent tutoring system. Real-time facial expressions were analyzed through recurrence quantification analysis alongside an examination of electrodermal activities (EDA) across the SRL phases. The findings reveal that emotion stability varied across SRL phases, with students exhibiting more stable emotions during the performance phase. Compared to the forethought and self-reflection phases, students had less frequent and lower intensity of emotional arousal in the performance phase. Moreover, we found that students with better performance demonstrated more stable emotions in the forethought phase, less stable emotions in the self-reflection phase, and a higher level of emotional arousal in the self-reflection phase. These insights highlight the temporal and dynamic nature of emotions in SRL, offering methodological and educational implications for leveraging facial expressions and EDA to monitor and enhance students' emotional experience during problem-solving.