In order to improve the combustion and emissions for high-speed marine diesel engines, numerical investigations on effects of different combustion chamber structures combined with intake air humidification have to be conducted in this paper. The study uses AVL Fire code to establish three-dimensional combustion model and simulate the in-cylinder flow, air-fuel mixing and combustion process with the flow dynamics metrics such as swirl number and uniformity index, analyze the interactional effects of combustion chamber structures and intake air humidification against the experimental data for a part load operation at 1350 r/min, find the optimized way to improve engine performance as well as decrease the NOx and soot emissions. The novelty is that this study is to combine different air humidifying rates with different combustion chamber structures including the re-entrant chamber, the straight chamber and the open chamber. Results show that the chamber diameter, bowl depth, intake air humidification can greatly influence in-cylinder flow, the re-entrant chamber makes a higher power output at the price of a smaller increase of NOx emissions, meanwhile the chamber combined with suitable humidifying rates can reduce the in-cylinder peak pressure and temperature and decrease the NOx emissions and cause a little more the soot emissions. The straight chamber has a lower emission at the same output power level compared with the prototype, the open chamber is found to have a lower out-put power.