Image registration is one of the important parts in medical image processing and intelligent analysis. The accuracy of image registration will greatly affect the subsequent image processing and analysis. This paper focuses on the problem of brain image registration based on deep learning, and proposes the unsupervised deep learning methods based on model decoupling and regularization learning. Specifically, we first decompose the highly ill-conditioned inverse problem of brain image registration into two simpler sub-problems, to reduce the model complexity. Further, two light neural networks are constructed to approximate the solution of the two sub-problems and the training strategy of alternating iteration is used to solve the problem. The performance of algorithms utilizing model decoupling is evaluated through experiments conducted on brain MRI images from the LPBA40 dataset. The obtained experimental results demonstrate the superiority of the proposed algorithm over conventional learning methods in the context of brain image registration tasks.