Submerged waterjet propulsion is a variant of conventional waterjet propulsion,whose inlet duct is fully integrated into the bottom plate of hull,reulting in a more complex coupled flow field behind.In order to meet the development requirements of submerged waterjet propulsion,the differences in mechanical control system between two types of waterjet propulsion were studied.Numerical simulations were conducted for both conventional and submerged waterjet propulsion at designed speed point.The comparison results show that submerged waterjet propulsion has larger flow obtaining area,higher inlet duct efficiency and less impact on the ship motion while the thrust reduction fraction is larger.