Affine registration can fit the non-rigid deformation of slices effectively, and it is widely used in volume reconstruction of biological tissue. But most of the existing affine registration methods are registered in a given sequence, which results in the accumulation of errors. In this paper, a global optimized affine registration method is proposed, which can be used in volume reconstruction. To eliminate the cumulative error, the affine transformation of all images is estimated simultaneously based on an energy function. A constraint on affine transformation is added to restrict the shearing of images. Experiments show that our method provides a more reliable registration result compared with sequential affine registration. It can solve the problems caused by the accumulation of errors. The registration result fits the deformation of slices well and preserves the rigidity of images.