The purpose of this study aimed to analyze the process of online collaborative problem solving (CPS) via brain-to-brain synchrony (BS) at the problem-understanding and problem-solving stages. Aiming to obtain additional insights than traditional approaches (survey and observation), BS refers to the synchronization of brain activity between two or more people, as an indicator of interpersonal interaction or common attention. Thirty-six undergraduate students participated. Results indicate the problem-understanding stage showed a higher level of BS than the problem-solving stage. Moreover, the level of BS at the problem-solving stage was significantly correlated with task performance. Groups with all high CPS skill students had the highest level of BS, while some of the mixed groups could achieve the same level of BS. BS is an effective indicator of CPS to group performance and individual interaction. Implications for the online CPS design and possible supports for the process of online CPS activity are also discussed.