Medical image alignment is an important research field in medical image processing, which is widely used in clinical diagnosis and treatment, such as surgical navigation, lesion tracking, and treatment evaluation. In this paper, an improved algorithm combining the Demons algorithm and SIFT algorithm is proposed, which uses the SIFT algorithm to represent the feature points in non-rigid medical images as a scale space sequence and normalize the descriptors in the scale space sequence. Then, the two-way alignment strategy and multi-resolution strategy are introduced to improve the accuracy of Demons algorithm in the alignment of non-rigid medical images with complex deformation. The study shows that the improved Demons algorithm can achieve better alignment results when the weights of the feature matching terms are taken as −1 and 1, which makes the improved Demons algorithm with the addition of SIFT feature terms perform optimally. Alignment simulation experiments found that the MSE value of this paper’s improved algorithm is only 0.077. The alignment effect of non-rigid medical images is much better than the comparison algorithm and can maintain a shorter running time. The algorithm in this paper can effectively realize the non-rigid alignment of medical images, which provides a reference method for medical diagnosis and the effective formulation of treatment plans.