Using AFM and traditional SEM, the authors studied the super-microscopic structure of pearls from micron-size to nanometer-size by observing the surfaces of pearls with different qualities, and discussed the correlation between the nanometer-size surface structure invisible with SEM and the physical properties (luster, roughness and concomitant color) of pearl. The research shows that the grade of pearl has a positive correlation with ordering and compactness of layers, microlayers, blocks and aggregates of aragonite. It is also suggested that quantified standard should be added to the classification for cultivation and trade of pearls by using such data as the mean roughness (Ra).