In the research of flow and heat transfer of the diesel engine cooling system, the boundary condition determination was often a difficult problem. The paper calculated the flow velocity and convective heat transfer coefficient respectively for a six-cylinder diesel engine under different boundary conditions which including the water jacket wall as adiabatic condition, average temperature condition, and the boundary conditions from the solid-fluid coupling calculating. And the calculated values of the jacket wall temperatures were compared with that of test. The results showed that the simulation with solid-fluid coupling boundary conditions had better precision. Based on the research, an improved structure design was conducted for the six-cylinder diesel engine, the results of simulation showed that the average flow speed at the internal surface of water jacket could reach up to 0.5m/s, the flow symmetry in each jacket got improved, and the convective heat transfer coefficient could reach more than 2000 W/m2·K. The improved cooling system can meet the design requirements.