While integrated delivery of anatomy and radiology can support undergraduate anatomical education, the interpretation of complex three-dimensional spatial relationships in cross-sectional and radiological images is likely to be demanding for novices. Due to the value of technology-enhanced and multimodal strategies, it was hypothesized that simultaneous digital and physical learning could enhance student understanding of cross-sectional anatomy. A novel learning approach introduced at a United Kingdom university medical school combined visualization table-based thoracic cross-sections and digital models with a three-dimensional printed heart. A mixed-method experimental and survey approach investigated student perceptions of challenging anatomical areas and compared the multimodal intervention to a two-dimensional cross-section control. Analysis of seven-point Likert-type responses of new medical students (n = 319) found that clinical imaging (mean 5.64 SD ± 1.20) was significantly more challenging (P < 0.001) than surface anatomy (4.19 ± 1.31) and gross anatomy (4.92 ± 1.22). Pre-post testing of students who used the intervention during their first anatomy class at medical school (n = 229), identified significant increases (P < 0.001) in thoracic cross-sectional anatomy interpretation performance (mean 31.4% ± 15.3) when compared to the subsequent abdominal control activity (24.1% ± 17.6). Student test scores were independent of mental-rotation ability. As depicted on a seven-point Likert-type scale, the intervention may have contributed to students considering cross-sectional interpretation of thoracic images (4.2 ± 1.23) as significantly less challenging (P < 0.001) than comparable abdominal images (5.59 ± 1.14). These findings could have implications for how multimodal cross-sectional anatomy learning approaches are implemented within medical curricula.