In order to improve the overall performance of medical image non-rigid registration, this paper presents a new medical image non-rigid registration method based on the LBM (Lattice Boltzmann Method). Firstly, this paper transforms medical image registration into a viscous fluid physical problem to take advantage of the fact that fluid particle movement can simulate any free complicated deformation. In the registration process of this paper, floating image, the gray level difference between the template image and the floating image, and image pixels are considered as a viscous fluid, external force and fluid particle, respectively. The external force from the gray level difference between the template image and the study image drives registration. Through simulation by use of the LBM, the flow of template image pixels under the external force which make the template image generate displacement field and deformation is obtained. When the gray scale values between the study image and the template image are near agreement the image registration has finished, at which time the external force disappears and the fluid flow stops. The LBM equation of the compressible viscous fluid with the external force is set up. In addition, the boundary conditions, initial conditions and speed module value are defined in this paper. Experimental results show that the non-rigid medical image registration performance has been improved comprehensively and especially the efficiency of image registration has a qualitative leap. This method is very suitable for large deformation registration occasions.