Variation of mesoscopic pore structure for soft soils is the primary cause of the macroscopical deformation. In order to study the variation of mesoscopic pore structure of soft soil as well as the correlative mechanism with macroscopical deformation during electro-osmosis, some electro-osmotic experiments were performed using Hangzhou soft soils. Pore structure distribution features and water contents of the soils were monitored during the experiments. The results were explained from the qualitative and quantitative perspectives. Clay particles were re-arranged into sheet-packed structure with plane-plane surfaces. The soil pore contracted, with resulted to decreasing of the void ratio, meanwhile the pores turned smoother in spatial forms and less complex in structure. Moreover, void ratios of the soil were computed through water content and the results were smaller than the measured values, which illustrated the electro-osmotic dewatering was larger than compression amount of soil. The fundamental cause goes to the fact that electro-osmosis derives from the migration of water dragged by ions and fails to generate compression of the soil skeleton directly. Electro-osmosis is recommended to be combined with surcharge and vacuum preloading in real practice.