Flexible air chamber jig is a new type jig, which has a wide application prospect. The stratification process of flexible air chamber jig was analyzed with discrete element method and computational fluid dynamic (DEM-CFD) model. Compared with other models, it can track the free surface and is closer to the actual situation. The analysis results were compared with the experimental results. The comparative results showed that the numerical analysis results were close to the experimental results, and the numerical analysis method was reasonable. For different stages of jigging, the stratification process and force of jigging particles were studied. According to the analysis results, the fluid plays different roles in different stages of particle movement. In the rising process, light particles were greatly affected by the fluid force, the time of this stage is important to stratification. The particle movement trajectory and stratification speed under different intake times was discussed, and it is concluded that intake time more than 18% of jigging cycle is reasonable.