In-depth characterization and understanding of multi-element airfoil flow structure is important to the design of multi-element airfoil shapes. Based on numerical simulation, the proper orthogonal decomposition (POD) method was used for reconstruction and analysis of numerical results of the multielement airfoil. With changes in the attack angle, the main modes of the flow are extracted, and their weight function with attack angle variation obtained. According to the simulation of flow field with an overlapped grid, a method that avoids ineffective impact on the analysis results is used by sifting the points in snapshots, and returning other points to the original position. It is found that the pulse stream flow sites account for a relatively small proportion of the total energy. The energy spectrum of the overall convergence of POD shows a slow-down pattern after a large-scale flow structure. Flow field in most of the energy distribution is directly related to the large scale flow sites included in the low-order modes, while the higher modes represent a complex pulse structure.