In this paper, the shrinkage characteristic curves (SSC) of Sanmenxia clay (SmC), Denver clay rock (DCs) and Zhengzhou silt (ZS) without external load were carried out. It is found that the shrinkage process of remolded soil does not show the traditional three stages. DCs show a non-zero shrinkage stage at low saturation, while SmC and ZS still conform to the three-stage law. Based on the theoretical model, the real pore water pressure is introduced to construct the calculation formula of intergranular stress σʹI, and the evolution law of intergranular stress with saturation during dehumidification is quantitatively revealed. The results show that the internal mechanical mechanism of shrinkage deformation is that the intergranular stress drives shrinkage and σʹI increases continuously with the decrease of saturation. Physicochemical effects dominated non-zero shrinkage, and DCs still had significant shrinkage when Sr < 27.5% due to high cation exchange capacity and surface physicochemical effects. The increase of bulk modulus inhibits the deformation under high stress, resulting in a smooth transition of void ratio of SmC when Sr > 95.8%. This study provides a theoretical basis for revealing the coupling mechanism of shrinkage-consolidation of unsaturated soil and the prevention and control of engineering disasters.