This mixed-method study introduced an adaptive scaffolding system to support middle school science problem-based learning (PBL) activities. 298 6th-graders were grouped into three conditions, which are the adaptive scaffolding group, the non-adaptive scaffolding group, and a control group that did not receive any scaffoldings. Results showed that problem-solving self-efficacy for students who engaged with the adaptive scaffolding system had improved significantly compared to the other two groups. Moreover, since students were conducting the PBL activity under two modes (online and in-person), the results also showed that students in the online mode gained more science content knowledge compared to their peers in the in-person mode after engaging with the adaptive system. Student interviews revealed that the real-time supports and in-time feedback provided by the adaptive system were the key elements that facilitated their improvements, teacher interviews presented that the adaptive system provided effective assists for teachers to facilitate the PBL activities.