The human pelvis is one of the skeletons where sex differences are expressed, but few detailed studies have been conducted on sex-related differences in the sacroiliac joint morphology. Therefore, we conducted a three-dimensional morphological analysis evaluation of the sacroiliac joints to clarify the sex-related difference of the joint's morphology. Right-side macerated innominate bones of Japanese males (n = 100) and females (n = 70) whose ages at death were recorded were included in the study. Three-dimensional images were created from the subjects' iliac auricular surface images, and 16 measurement parameters were acquired on the basis of 11 defined measurement points. All measurement parameters were compared between the male and female groups. The values of the measurement parameters indicating the size of the iliac auricular surface were significantly larger in the male group than in the female group. In addition, the angle between the short and long arms of the auricular surface was larger in the male group. Furthermore, on the basis of the corrected values of the physical disparity, the long arm dimension of the iliac auricular surface was larger in the male group, while the short arm dimension was larger in the female group. The sex-based differences in the iliac auricular surface morphology that were confirmed in this study may reflect the sex-based differences in the sacroiliac joint function. The findings of this study may contribute to the elucidation of the pathophysiology of the sacroiliac joint dysfunction that frequently occurs in women.