Medical image segmentation (IS) is a research field in image processing. Deep learning methods are used to automatically segment organs, tissues, or tumor regions in medical images, which can assist doctors in diagnosing diseases. Since most IS models based on convolutional neural network (CNN) are two‐dimensional models, they are not suitable for three‐dimensional medical imaging. On the contrary, the three‐dimensional segmentation model has problems such as complex network structure and large amount of calculation. Therefore, this study introduces the self‐excited compressed dilated convolution (SECDC) module on the basis of the 3D U‐Net network and proposes an improved 3D U‐Net network model. In the SECDC module, the calculation amount of the model can be reduced by 1 × 1 × 1 convolution. Combining normal convolution and cavity convolution with an expansion rate of 2 can dig out the multiview features of the image. At the same time, the 3D squeeze‐and‐excitation (3D‐SE) module can realize automatic learning of the importance of each layer. The experimental results on the BraTS2019 dataset show that the Dice coefficient and other indicators obtained by the model used in this paper indicate that the overall tumor can reach 0.87, the tumor core can reach 0.84, and the most difficult to segment enhanced tumor can reach 0.80. From the evaluation indicators, it can be analyzed that the improved 3D U‐Net model used can greatly reduce the amount of data while achieving better segmentation results, and the model has better robustness. This model can meet the clinical needs of brain tumor segmentation methods.