The traditional approach of using PowerPoint (PPT) presentations in medical imaging theory classes hinders the spatial thinking ability of most students. Consequently, the learning outcomes are often unsatisfactory. This article proposes a naked eye three-dimensional (3D) medical imaging teaching assistant app based on augmented reality (AR) technology to enhance learning interest, teaching interaction, and effectiveness. The control group consisted of 50 undergraduate students from the 2018 clinical medicine major who receive traditional teaching, while the experimental group includes 52 undergraduate students from the 2019 cohort who utilize an AR-based naked eye 3D teaching assistant app in addition to traditional teaching methods. Based on Bloom's cognitive learning taxonomy ("Remember, Understand, Apply, Analyze, Evaluate, and Create"), corresponding teaching curricula and assessment methods were designed in order to achieve more in-depth learning of the curriculum. The evaluation of the teaching effectiveness between the two groups relied on exam scores and student satisfaction questionnaires, with statistical analyses conducted using t-test and Mann-Whitney U-test in SPSS. The experimental group and control group showed statistically significant differences in the theoretical examination scores (62.06 ± 3.06 vs. 59.82 ± 3.38), practical testing scores (22.90 ± 2.35 vs. 21.06 ± 2.65), and total scores (84.96 ± 4.58 vs. 80.88 ± 6.01). Likert scores showed the experimental group scored significantly higher in enjoyment, satisfaction, participation, efficiency, and understanding. They also reported high convenience scores for the app and desired continued use. The naked eye 3D teaching assistant system is an innovative and effective teaching model for undergraduate medical imaging education, enhancing student interest, student interaction, and teaching effectiveness and promising future applications.