Current studies of a seawater axial piston pump mainly solve the problems of corrosion and wear in a slipper pair by selecting materials with corrosion resistance, self-lubrication, and wear resistance. In addition, an appropriate biomimetic non-smooth surface design for the slipper pair can further improve the tribological behavior. In this paper, 316L stainless steel and CF/PEEK were selected to process the upper and bottom specimens, and the biomimetic non-smooth surface was introduced into the interface between the friction pair. The friction and wear tests were performed on a MMD-5A tester at a rotation speed of 1000 r/min and load of 200 N under seawater lubricated condition. The results indicate that the main friction form of the smooth surface friction pair corresponds to abrasive wear and adhesive wear and that it exhibits a friction coefficient of 0.05-0.07, a specimen temperature of 56 °C, a high wear rate, and surface roughness. Pits on the non-smooth surface friction pairs produced hydrodynamic lubrication and reduced abrasive wear, and thus the plowing effect is their main friction form. The non-smooth surface friction pairs exhibit a friction coefficient of 0.03-0.04, a specimen temperature of 48 °C, a low wear rate, and surface roughness. The study has important theoretical significance for enriching the lubrication, friction, and wear theory of a seawater axial piston pump, and economic significance and military significance for promoting the marine development and the national defense military.