Anatomy is the cornerstone of medical education. Virtual reality (VR) and augmented reality (AR) technologies are becoming increasingly popular in the development of anatomy education. Various studies have evaluated VR and AR in anatomy education. This meta-analysis aims to evaluate the effectiveness of VR and AR in anatomical education. The protocol was registered in Prospero. Scopus, PubMed, Web of Science, and Cochrane Library databases were searched. From the 4487 articles gathered, 24 randomized controlled trials were finally selected according to inclusion criteria. According to the results of the meta-analysis, VR had a moderate and significant effect on the improvement of knowledge scores in comparison with other methods (standardized mean difference = 0.58; 95% CI = 0.22, 0.95; p < 0.01). Due to the high degree of heterogeneity (I2 = 87.44%), subgroup analyses and meta-regression were performed on eight variables. In enhancing the "attitude," VR was found to be more "useful" than other methods (p = 0.01); however, no significant difference was found for "enjoyable" and "easy to use" statements. Compared with other methods, the effect of AR on knowledge scores was non-significant (SMD = -0.02; 95% CI = -0.39, 0.34; p = 0.90); also, in subgroup analyses and meta-regression, the results were non-significant. The results indicate that, unlike AR, VR could be used as an effective tool for teaching anatomy in medical education. Given the observed heterogeneity across the included studies, further research is warranted to identify those variables that may impact the efficacy of VR and AR in anatomy education.