The presentation of pre‐sliced specimens is a frequently used method in the laboratory teaching of cross‐sectional anatomy. In the present study, a new teaching method based on a hands‐on slicing activity was introduced into the teaching of brain, heart, and liver cross‐sectional anatomy. A randomized, controlled trial was performed. A total of 182 third‐year medical students were randomized into a control group taught with the prosection mode (pre‐sliced organ viewing) and an experimental group taught with the dissection mode (hands‐on organ slicing). These teaching methods were assessed by testing the students' knowledge of cross‐sectional specimens and cross‐sectional radiological images, and analyzing students' feedback. Using a specimen test on three organs (brain, heart, and liver), significant differences were observed in the mean scores of the control and experimental groups: for brain 59.6% (±14.2) vs. 70.1% (±15.5), (P < 0.001, Cohen's d = 0.17); for heart: 57.6% (±12.5) vs. 75.6% (±15.3), (P < 0.001, d = 0.30); and for liver: 60.4% (±14.5) vs. 81.7% (±14.2), (P < 0.001, d = 0.46). In a cross‐sectional radiological image test, better performance was also found in the experimental group (P < 0.001). The mean scores of the control vs. experimental groups were as follows: for brain imaging 63.9% (±15.1) vs. 71.1% (±16.1); for heart imaging 64.7% (±14.5) vs. 75.2% (±15.5); and for liver imaging 61.1% (±15.5) vs. 81.2% (±14.6), respectively. The effect sizes (Cohen's d) were 0.05, 0.23, and 0.52, respectively. Students in the lower tertile benefited the most from the slicing experiences. Students' feedback was generally positive. Hands‐on slicing activity can increase the effectiveness of anatomy teaching and increase students' ability to interpret radiological images.