In order to get fully understanding of the interior flow field of a two-stage filtration system composed of sand filter and screen filter in irrigation system, the interior flow field was analyzed and offered optimization by building 3D model using Pro/Engineer, based on computational fluid dynamics (CFD) technique, numerical simulation and using RNG k-εmodel combined with porous media model. And the new integrated filter was made and the performance test it was done. As it was shown in the result, simulation results of the RNG k-εmodel were consistent with the experimental results. Therefore, the model can be used for flow field analysis and structural optimization. When the combined filter system was set with sand filtration material and screen mesh separately installed in different shells, it would cause huge water head loss due to the influence of pipes between sand filter and screen filter and shell of screen filter. And too much circulation and whirlpool of water inside the filter due to complexity of structure led to instability of flow field, which finally caused uneven distribution of velocity during filtering. In terms of the shortcoming of traditional combination filter system based on field flow analysis, a new type of integrated layout optimization incorporating the screen into the sand filter was proposed to improve the complexity of the layout. According to the field flow analysis, integrated filter’s water head loss was decreased by 38.5%, and interior field flow was more stable because the tank space was larger and the flow disturbance was smaller. And the flow velocity distribution was more uniform during filtering, so the utilization of the screen was more reasonable, and the screen life of the filter was extended. After the comparison of two performance tests, it was known that the new integrated filter can effectively reduce the loss of water head and it can run about 20min more when the flow rate was decreased by 20% under the condition of sand water. It was showed that the new integrated filter’s hydraulic performance was better and the irrigation efficiency was improved. According to the research raised above, a kind of digital method was proposed to discuss the performance of the filter, which was used to research and design a kind of integrated filter, and finally the advantageous structure of the integrated filter was obtained, including the sand filter and the screen filter.