Morphological changes in neurodegenerative diseases can be detected with structural MR images, but it requires detailed brain parcellation. Therefore, a task-aware V-Net was proposed to segment the brain into 40 regions. Task-aware features were achieved by three cascading branches, including brain and non-brain regions, 25 regions with the bilateral regions grouped, and 40 regions, respectively. The proposed model was developed on 8938 subjects and validated using additional196 subjects. The proposed method outperformed the typical 3D U-Net and V-Net, and achieved state-of-the-art results on both datasets with a mean Dice score of 0.886 ± 0.029 and 0.874 ± 0.013, respectively.