Anatomy is shifting toward a greater focus on adopting digital delivery. To advance digital and authentic learning in anatomy, a flipped classroom model integrating multimodal digital resources and a multimedia group assignment was designed and implemented for first-year neuroanatomy and third-year regional anatomy curricula. A five-point Likert scale learning and teaching survey was conducted for a total of 145 undergraduate health science students to evaluate students' perception of the flipped classroom model and digital resources. This study revealed that over two-thirds of participants strongly agreed or agreed that the flipped classroom model helped their independent learning and understanding of difficult anatomy concepts. The response showed students consistently enjoyed their experience of using multimodal digital anatomy resources. Both first-year (75%) and third-year (88%) students strongly agreed or agreed that digital tools are very valuable and interactive for studying anatomy. Most students strongly agreed or agreed that digital anatomy tools increased their learning experience ([approximately]80%) and confidence (> 70%). The third-year students rated the value of digital anatomy tools significantly higher than the first-year students (p = 0.0038). A taxonomy-based assessment strategy revealed that the third-year students, but not the first-year, demonstrated improved performance in assessments relating to clinical application (p = 0.045). In summary, a flipped anatomy classroom integrating multimodal digital approaches exerted positive impact upon learning experience of both junior and senior students, the latter of whom demonstrated improved learning performance. This study extends the pedagogy innovation of flipped classroom teaching, which will advance future anatomy curriculum development, pertinent to post-pandemic education.