Abstract: To ascertain the influential mechanisms of the microstructure for soft soil on the macroscopic mechanical properties, consolidation shear tests of mucky soil in Nansha zone of Guangzhou were conducted. Combined with the scanning electron microscope and the microscopic tomography technique, the microstructure changes of the upper and lower parts for specimens and the influential mechanisms on the shear strength were qualitatively and quantitatively analyzed. The results showed that the void ratios of the soft soil gradually decreased with the continuous increase of consolidation pressure, and the final void ratios were mostly between 0.5 to 0.6. There were obvious inflection points for void ratios, and the values of lg(p/kPa) were mostly between 1.5 and 2.0. After shear failure, the moisture contents of the soil specimens from lower locations were significantly higher than that from of the upper, and the differences ranged from 1.8% to 3.3%.The cohension values of mucky soil had little relation with the initial moisture contents of the specimens, and the values of angles for internal friction were about 14° measured by quick direct shear tests. From the perspective of spatial structure, Nansha mucky soil had a variety of structural types, including honeycomb, spongy and flocculent structure, as well as flake, skeleton and agglomerate structure. The contact modes were mainly face-face, face-side, angle-face and angle-angle. The response mechanisms of consolidation pressure, free water and particles could well explain phenomena of engineering silting.