Cranial defects may result from clinical brain tumor surgery or accidental trauma. The defect skulls require hand-designed skull implants to repair. The edge of the skull implant needs to be accurately matched to the boundary of the skull wound with various defects. For the manual design of cranial implants, it is time-consuming and technically demanding, and the accuracy is low. Therefore, an informer residual attention U-Net (IRA-Unet) for the automatic design of three-dimensional (3D) skull implants was proposed in this paper. Informer was applied from the field of natural language processing to the field of computer vision for attention extraction. Informer attention can extract attention and make the model focus more on the location of the skull defect. Informer attention can also reduce the computation and parameter count from N2 to log(N). Furthermore,the informer residual attention is constructed. The informer attention and the residual are combined and placed in the position of the model close to the output layer. Thus, the model can select and synthesize the global receptive field and local information to improve the model accuracy and speed up the model convergence. In this paper, the open data set of the AutoImplant 2020 was used for training and testing, and the effects of direct and indirect acquisition of skull implants on the results were compared and analyzed in the experimental part. The experimental results show that the performance of the model is robust on the test set of 110 cases fromAutoImplant 2020. The Dice coefficient and Hausdorff distance are 0.940 4 and 3.686 6, respectively. The proposed model reduces the resources required to run the model while maintaining the accuracy of the cranial implant shape, and effectively assists the surgeon in automating the design of efficient cranial repair, thereby improving the quality of the patient’s postoperative recovery.