It is necessary for keeping Autonomous Underwater Vehicle (AUV) on station to realize AUV docking underwater for AUV charging, data transferring and checking. While the flow field in AUV underwater docking is coupled caused by multi-body moving, which is a difficult problem for Computational Fluid Dynamics (CFD) to solve. Hybrid dynamic grids method has been presented in simulating AUV docking with a torpedo shaped tube. A mesh topology including hybrid grids domain is built which including hexahedral, prismatic and tetrahedral grids. With the motion of AUV, dynamic layering method is used to update mesh. Compared with spring analogy and local re-meshing method, Dynamic layering method significantly improves the robustness for problems with large motions of bodies without much penalty in CPU time during remeshing. The numerical result gets pressure contours at different time, and the resistant coefficient of AUV during docking processes for more than 10 meters, the resistance when AUV at unbounded domain solved by this method agrees well with that of coordinate transformation method. This research is not only helpful for improving control resolution in AUV underwater docking with tube, but also get a method to solve the hydrodynamics for multi-body moving relatively, which is popular in ocean engineering.