Segregation resistance is an important index for evaluating the workability of fresh concrete. Considering the real shape of aggregates in self-compacting concrete, the three-dimensional random aggregate modeling is realized. The GMO (General Moving Object) method was used to simulate the motion and static segregation of fresh self-compacting concrete as a two-phase solid-liquid medium mixed with coarse aggregates and mortar. The effect of yield stress and viscosity of mortar on aggregate movement process was studied. Based on this, the movement behavior of three groups of self-compacting concrete coarse aggregates with different gradation in mortar was studied. The results show that the yield stress of mortar has an obvious effect on the static segregation of concrete, while the viscosity has little effect. The segregation behavior of different aggregate gradations under the same conditions is different, but it still shows certain regularity. Under the same conditions, gradation with less content of large particle size aggregate and more content of small particle size aggregate was relatively stable.