The invention provides a continuous brain slice image three-dimensional registration method based on shape constraint, and relates to the technical field of image registration. The method comprises the following steps: S1, aligning a to-be-registered two-dimensional brain image sequence to obtain a two-dimensional alignment sequence, and reconstructing the two-dimensional alignment sequence into an initial three-dimensional body; S2, linearly registering the standard brain atlas to the initial three-dimensional body to obtain a reference brain atlas, registering pictures of the two-dimensionalalignment sequence to tangent planes of corresponding positions in the reference brain atlas one by one to obtain a two-dimensional correction sequence, and reconstructing a corrected three-dimensional body; and S3, obtaining reverse deformation parameters of each pixel point in the corrected three-dimensional body, and performing spatial offset adjustment on the corrected three-dimensional bodyaccording to the reverse deformation parameters to obtain a refined three-dimensional body. The reference brain atlas is used as a constraint condition of the global shape, so that the correct shape of the real brain tissue is introduced into correction three-dimensional body reconstruction, and the problem of axial offset caused by lack of a spatial position relationship and global shape information in the prior art is solved.