The mesostructure of soft soil has important influence on the consolidation process，it is of great guiding significance to consider soft soil structure from meso level and reveal the law of consolidation in a large area of reclamation project. In this paper, we establish the soil mesoscale model based on the discrete element method, match mesoscale parameters of the model according to the laboratory test, analyze the distribution of the seepage field in the soil body with COMSOL, realize to solve the consolidation problem of soft soil with PFC-COMSOL, and compare the analysis scheme with the laboratory test. Research results show that simulating flocculation soft soil with poly grain can truly react mesostructure characteristics of soft soil; Creep can influence the decrement in the process of consolidation of soft soil, creep should be considered in calculating the amount of soft soil compression; Uneven compression appears firstly in the process of consolidation of soft soil, after the excess pore pressure is dissipated completely, the soil recovers uniformity.