Three-dimensional (3D) ground-penetrating radar is an effective method for detecting internal crack damage in pavement structures. Inefficient manual interpretation of radar images and high personnel requirements have substantially restrained the generalization of 3D ground-penetrating radar. An improved Crack Unet model based on the Unet semantic segmentation model is proposed herein for 3D ground-penetrating radar crack image processing. The experiment showed that the MPA, MioU, and accuracy of the model were improved, and it displayed better capacity in the radar image crack segmentation task than current mainstream algorithms do, such as deepLabv3, PSPNet, and Unet. In the test dataset without cracks, Crack Unet is on the same level as deepLabv3 and PSPNet, which can meet engineering requirements and display a significant improvement compared with Unet. According to the ablation experiment, the MPA and MioU of Unet configured with PMDA, MC-FS, and RS modules were larger than those of Unet configured with one or two modules. The PMDA module adopted by the Crack Unet model showed a higher MPA and MioU than the SE module and the CBAM module did, respectively. The results show that the Crack Unet model has a better segmentation ability than the current mainstream algorithms do in the task of the crack segmentation of radar images, and the performance of crack segmentation is significantly improved compared with the Unet model. The Crack Unet model has excellent engineering application value in the task of the crack segmentation of radar images.