Background: Three-dimensional (3D) printing is an emerging technology widely used in medical education . However, its role in the teaching of human anatomy needs further evaluation. This st udy compared 3D printed models with conventional models to provide a better understanding of their use in the teaching of anatomy. Methods: PubMed, Embase, EBSCO, SpringerLink, and Nature databases were searched systematically for studies published up to April 2020 in the English language. This study complies with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. In this study, a meta-analysis of continuous and binary data was carried out. Both descriptive and statistical analysis were adopted. Results: In the teaching of human anatomy, compared with students in the conventional group, those in the 3D printing group showed several advantages in performance testing, time consumption, students’ intention, and usefulness. The leave-one-out method further confirmed the stability of the results. Conclusions: Compared with students in the conventional group, those in the 3D printing group had advantages in answering accuracy and answering time. In the test of anatomical knowledge, the test results of students in the 3D group were not inferior to those in the traditional group. Results of the autopsy test in the 3D group were better than those in the cadaver or 2D group. More students in the 3D printing group were satisfied with their learning compared with students in the conventional group. The results were influenced by the quality of randomized controlled trials. In the framework of abiding by ethics, the application of the 3D printing model in human anatomy teaching is worthy of expectation.