With the development of society and economy, land subsidence in soft soil areas has become a prominent geological disaster in our country’s coastal area. Land subsidence has the characteristics of irreversibility, wide influence range, long aging, etc., and these characteristics are closely related to the characteristics of soft soil, such as physical and mechanical parameters, microstructure characteristics, etc. The Nansha District of Guangzhou was taken as the study area in this paper. Through the collection of preliminary data, two-dimensional scanning electron microscopy, and three-dimensional Computed Tomography (CT), the micro-structure characteristics of soft soil are expounded and its plugging characteristics are further analyzed. The results show that the study area’s soft soil has a honeycomb, granular, and flocculent structure. From the perspective of pore scale distribution, the number of macropores and ultramicro pores is small, and the continuity is poor. In most small and medium pores, namely the aggregate and granular pores. The siltation of soft soil is closely related to the microstructure of soil and can be treated according to the effect of siltation characteristics on the consolidation settlement of soft soil. The research results of this paper can provide targeted prevention and control suggestions for the soft land subsidence disaster in the Nansha area, and also provide a reference for other similar research.