This paper aims to characterize the three-dimensional (3D) internal structure evolution of asphalt mixtures under freeze–thaw cycles. Asphalt mixtures with three levels of design void content (3%, 5%, and 7%) were prepared in the laboratory. Subsequently, X-ray computed tomography (CT) tests were conducted to capture two-dimensional (2D) images of the internal structure of samples before and after freeze–thaw testing. A set of image processing techniques for reconstructing 3D images of the internal structure were utilized to extract the internal structure properties, which were then used to analyze the changes in the air void distributions and to evaluate the internal structure evolution under freeze–thaw cycles. 3D images reconstructed from X-ray CT images illustrated a dramatic degradation in the internal structure after cyclic freeze–thaw exposure. The change in internal structure occurs mainly in three ways: (1) expansion of existing individual voids, (2) combination of two separated air voids, and (3) generation of new voids. In addition, the parametric analysis of the three-dimensional reconstructed voids revealed that the asphalt mixture void ratio increased with the number of freeze–thaw cycles, while the larger the initial void content, the more pronounced the increase in the specimens. Therefore, asphalt mixture freeze–thaw resistance should be optimized in relation to the design void content.