Abstract: Analysis result of scanning electron microscopy shows that Shanghai soft soil appears anisotropy in microstructure, and can be further subdivided into the original and secondary interstices by genesis. The original interstice is formed during flocculation and tends to be close or open by gravity action during concretion, which makes the horizontal interstice more permeable than the vertical one. The interstice formed either by groundwater dissolving the freely soluble grains in the aquifer or by seepage dynamic action reconstructing the existed interstice, is named as the secondary interstice, whose anisotropy is higher than that of the original interstice. The anisotropy of seepage is decided by the interstice's distribution and its anisotropy of connectivity, and seepage in the anisotropy medium will strengthen the characteristics of soft soil's microstructure and macrostructure anisotropy.