Aiming at the problem of poor accuracy of automatic region division of mouse brain slice image using traditional multimodal registration method,an unsupervised multimodal region division method of brain slice image was proposed. Firstly,based on the mouse brain map,the Atlas brain map and the Average Template brain map in the Allen Reference Atlases (ARA) database corresponding to the brain slice region division were obtained. Then the Average Template brain map and the mouse brain slices were pre-registered and modal transformed by affine transformation preprocessing and Principal Component Analysis Net-based Structural Representation(PCANet-SR)network processing. After that,according to U-net and the spatial transformation network,the unsupervised registration was realized,and the registration deformation relationship was applied to the Atlas brain map. Finally,the edge contour of the Atlas brain map extracted by the registration deformation was merged with the original mouse brain slices in order to realize the region division of the brain slice image. Compared with the existing PCANet-SR+B spline registration method,experimental results show that the Root Mean Square Error(RMSE)of the registration accuracy index of this method reduced by 1. 6%,the Correlation Coefficient(CC)and the Mutual Information(MI)increased by 3. 5% and 0. 78% respectively. The proposed method can quickly realize the unsupervised multimodal registration task of the brain slice image,and make the brain slice regions be divided accurately.