Abstract: When an underwater explosion occurs near both a free surface and a warship structure，the bubble motion could be affected. In this paper，the boundary integral equation was solved by adopting the boundary element method（BEM），based on the potential flow theory of incompressible liquid. To reduce the quantity of meshes required when modeling the free surface and to deal with the instability of solid-free surface interfaces，a Green function considering the free surface effect was adopt to replace the fundamental Green function. This numerical method was validated by comparing the above mentioned model with an axisymmetrical model. Also，the bubble motions as well as its jet feature near a warship structure and a free surface were simulated，and it was found out that the bubble jet would not significantly impact the warship structure because of the free surface effect.