With the CFD method and orthogonal experiment method, the hydrodynamic lubrication performance of port plate pairs with Bionic Non-smooth Surface has been analyzed. Under the condition of guaranteeing that the sum of all the pithead area surfaces is the same in different bionic non-smooth, full water flow deputy hydrodynamic lubrication models has been established. The effect of rotating speed, pit sectional shape and pithead diameter on hydrodynamic loading capacity with concave bionic non-smooth surfaces is explored. It concludes that the influence of the three factors are in turn as follows: rotating speed is more important than pithead diameter, and pithead diameter is more important than pit sectional shape. Bionic nonsmooth surface is suitable for relatively high-speed conditions. Different sizes of pithead diameter have a great impact on pit hydrodynamic pressure-loading capacity. As pithead diameter increases, so does the load-carrying capacity of conical pit, cylinder pit, truncated-conic pit and spherical pit within limits. Among those pits, the pressure-loading capacity of bionic nonsmooth surface with conical pit performs best when the pit diameter is 1.6mm. High pressure axial piston pump is widely applied in aircraft, to improve the loading capacity and anti-wear performance of the key tribopairs such swash plate/slipper, port plate/cylinder block and piston/cylinder block is very important for promoting the reliability and increasing service life of the axial piston pump. Bionic non-smooth surface effects studied and the method employed in this paper could be used in the investigation of the key tribopairs of high pressure axial piston pump used in aircraft.