Abstract: The thixotropy is one of rheological properties, and it is the phenomenon that the strength decreases owing to external force and then gradually increases with time after stopping disturbance. In order to explore the microscopic mechanism of strength increase of clay during thixotropic process, the unconfined compressive strength and penetration resistance of Zhanjiang clay after disturbance of 500 d are tested, the thixotropic strength evolution process is analyzed, and the thixotropic rules are determined according to the thixotropic strength ratio. Furthermore, microstructural change at different standing time is studied using the scanning electron microscope and mercury injection experiment. The results show that the thixotropic characteristics of Zhanjiang clay are significant, and the strength after 500 d is 2.58 times that after the disturbance, but the thixotropic increase strength only accounts for 21.2%~23.5% of the disturbance strength loss. Therefore, for the soils with high sensitivity and strong structure engineering disasters can not be ignored because of strength loss caused by construction disturbance. The thixotropic strength recovery is the result of the structural evolution from dispersion to flocculation through attraction and repulsion between particles owing to change of force field. In this process, the microstructure is self-adapted and pore distribution uniformly develops, and in a certain period of time the thixotropic phenomenon occurs.