Student engagement plays a vital role in improving students' learning outcomes. Traditional educational assessments of engagement have many limitations, which undermine the understanding of the mechanisms by which engagement affects learning and broad educational practices that leverage engagement. Through a mixed-methods approach and multimodal data collected in naturalistic high school classrooms, this study investigated the physiological characterization of student engagement and demonstrated its unique advantages of continually revealing students' implicit engagement during learning. Interpersonal physiological synchrony (IPS) seems to have higher criterion validity than intrapersonal physiological features, according to quantitative analysis. The quantitative results of the IPS are also better interpreted and triangulated by qualitative analysis. Challenges of real-world neuroeducational research are discussed, and the unique assets of mixed methods research are proposed.