For efficiency improvement and state monitoring of the propeller of a ship, a non-smooth surface is a conventional approach to reducing drag, saving energy, and providing a stabler sensing condition. In this paper, we studied the effects of the surface roughness and protrusions on propeller performance, and the hydrodynamic performance of a marine propeller, including the propeller thrust, torque, and open water efficiency, was analyzed for different surface conditions. By ANSYS meshing, the Y+ value of the rotating propeller was ensured to be less than 5. The shear stress transport (SST) turbulence model, stationary domain, and rotating domain were adopted to model the water flow during simulation in an ANSYS software CFX module. In our numerical calculations, there were four surface conditions for the rotating blade of the propeller: a non-slip smooth surface, a surface with a roughness of 5 μm, and surfaces with protrusions of 0.2 and 0.3 mm. The results show that the efficiency of the propeller is increased by protrusions located on the pressure surface. The propeller with 0.2 mm protrusions shows the best performance. Compared with the non-slip smooth wall condition, the thrust force is increased, and the increase in propeller efficiency is 2.83% when the advance coefficient of the propeller J is 0.9 and 6.40% when J is 1.0. The propeller efficiency is reduced by blade surface roughness, but the flow field is more stationary for the propeller with surface protrusions, which is beneficial for propeller shaft sensors. The other hydrodynamic parameters are also analyzed to illustrate their effect on the propeller performance.