The invention relates to the technical field of medical image processing, and provides a brain nuclear magnetic resonance image segmentation method and system. The method mainly comprises the steps of brain nuclear magnetic resonance image data preprocessing, brain nuclear magnetic resonance image segmentation model construction and optimization, brain nuclear magnetic resonance image segmentation and result output. The system comprises a computer processor, a memory, a brain nuclear magnetic resonance image preprocessing unit, a brain nuclear magnetic resonance image segmentation model training unit and a brain nuclear magnetic resonance image segmentation and result output unit. According to the method, firstly, a space structure network of brain nuclear magnetic resonance images is constructed, pixel point information of brain function tissue activation images can be recorded, the space structure relation between the pixel point information and the space structure network can be effectively expressed, and then a brain nuclear magnetic resonance image segmentation model is established through an image variation auto-encoder structure; therefore, the model has a certain generation capability and can obtain a brain nuclear magnetic resonance image segmentation result with higher robustness and interpretability.