In precise fuel circuit systems, the filtration of particulate impurities seriously affects the efficiency and service life of various components. For filtration process intensification of high-pressure fuel laser perforated filters, the two-phase flow characteristics in filters is studied. The size, position and number of filtration holes are taken as optimization variables, and take the filtration efficiency and flow pressure drop as optimization objectives. Computational fluid dynamics (CFD) is used to simulate the two-phase motion of continuous phase and discrete particles in a periodic unit. Artificial neural networks (ANN) are utilized for objectives prediction, and the NSGA-II genetic algorithm is employed for multi-objective optimization, resulting in the Pareto front solution set. Furtherly, the reasonable solution is selected by introducing TOPSIS to ensure that two optimization indexes are relatively smaller and balanced. The optimized filter element scheme allows the filter to have a pressure drop of less than 3.2 MPa under high pressure and a filtration efficiency of over 80% for spherical particle impurities with a diameter of 5 microns or more.