To achieve a better understanding of the evolution of the large brain in humans, a comparative analysis of species differences in the brains of extant primate species is crucial, as it allows direct comparisons of the brains. We developed a method to achieve anatomically precise region-to-region homologous brain transformations across species using computational neuroanatomy. Utilizing three-dimensional neuroimaging data from humans (Homo sapiens), chimpanzees (Pan troglodytes), and Japanese macaques (Macaca fuscata), along with the anatomical labels of their respective brains, we aimed to create a cross-species average template brain that preserves neuroanatomical correspondence across species. Homologous transformation of the brain from one species to another can be computed using the cross-species average brain. Applying this transformation to human and chimpanzee brains revealed that, compared to chimpanzees, humans had significantly larger and more expanded prefrontal cortex, middle and posterior temporal gyrus, angular gyrus, precuneus, and cortical areas associated with mentalization. This neuroanatomically homologous brain transformation enables the systematic investigation of the similarities and differences in brain anatomy and structure across different species.