The collision between the vessels during skin-to-skin connected replenishment was modeled based on the multibody dynamics with unilateral contacts and classical marine hydrodynamics. With additional water mass taken into account the collision force expression was deduced for the vessels without anti-impact protection device, and relevant numerical simulation was presented. In order to improve the efficiency, during simulation process the identification of practical constraints for non-smooth system was converted into an extremum problem and solved with optimization theory. The preliminary simulation results were conformed to those of the relevant experiments as a whole, which proves that the new calculation method for the collision is available for the design of the anti-impact protection device.