Introduction: Teaching human anatomy to produce deeper understandings and knowledge retention in learners requires meaningful, engaging, and practical activities. Previous studies identify that most students who participated in body painting (BP) reported improved understanding of surface anatomy (SA). This study investigates the key factors underpinning how BP helps students learn SA. Methods: The study involved an explanatory mixed-methods approach. Towards the end of an anatomy course, a survey was administered to three cohorts of first-year chiropractic, osteopathy, and Chinese medicine students and second-year biomedical sciences students over 3 years (n = 311; response rate = 30%). The survey assessed the effectiveness of BP as a hands-on, group-based approach for learning SA in practical class. Three student focus groups (n = 13) explored the key survey findings. Results: Overall, 72% of student respondents reported BP activities helped them learn SA “quite a bit” or “very much”. Multivariate analysis identified students found BP helped them learn SA by “remembering the position of the bones, joints, muscles, actions and insertions” (POR = 5.7; P < 0.001); “integrating textbook and other knowledge on a real live person” (POR = 2.4; P = 0.027); and “achieving a deeper understanding of SA” (POR = 5.2; P < 0.001). The qualitative findings describe specifically how BP helps students learn, understand, and remember SA. Conclusions: The findings show the majority of students believed BP benefitted their learning of SA through enhancing engagement in self-directed classroom and out-of-hours learning opportunities, deeper understandings of form and function, retention of knowledge, and practical physical examination experiences palpating the variations in form between individuals.