In Walker's nonmetric method, the nuchal crest serves as the representative region for indicating sexual dimorphism in cranial bones. However, the accuracy of sex estimation using the nuchal crest is lower than that using other anatomical regions. Furthermore, because of the protruding processes and structurally challenging features characterized by uneven and rough surfaces, there is a lack of metric methods for sex estimation, making quantification challenging. In this study, we aimed to validate a derived metric method for sex estimation by reconstructing the nuchal crest region in three-dimensional (3D) images obtained from computed tomography scans of cranial bones and compare its accuracy with that of the nonmetric method. A total of 648 images were collected, with 100 randomly selected for use in the nonmetric method. We applied our metric method to the remaining 548 images. Our findings showed that the surface area of the nuchal crests was greater in male individuals than in female individuals. The nuchal crest surface area quantified by the metric method increased the accuracy of sex estimation by 48% compared with that by the nonmetric method. Our metric method for sex estimation, which quantifies the nuchal crest surface area using 3D images of the skull, led to a high sex estimation accuracy of 93%. Future studies should focus on proposing and quantifying new measurement methods for areas showing sexual characteristics in the skull that are difficult to measure, thereby enhancing the accuracy and reliability of sex estimation in human skeletal identification across various fields.