The filter media with high efficiency, low resistance and long life, is attracting more and more attention in the environmental research. To boost the efficiency of developing fiber filter media, simulation research on its structure design and filtration performance is needed, as the traditional methods based on a large amount of experiments are time-consuming. Previous researches of fiber filter media model were mainly focused on the micron scale and rarely involved at the submicron scale. Based on the actual multi-dispersed submicron glass fiber and glass fiber filter media, this work established a three-dimensional model closer to the actual filter media structure from the characterization of glass fibers, the fabrication of filter media and its given structural parameters. By comprehensively comparing the simulation results with the actual performance of the filter media made by wet-laid process, the model's applicability to predict the performance of glass fiber filter media was thoroughly investigated. The experimental results showed: the average pore size of the filter model aligned with the actual experimental results; the calculated filtration resistance and filtration efficiency were closer to the experimental measurement results than those of the empirical model; the error in filtration efficiency was less than 1% (the simulated results of three filter media were 61%, 99.6% and 100% respectively, against the measured results of 60.5%, 99.1% and 99.96% of their actual samples). The structure model of the filter media and the mathematical model of the calculation performance have a wide range of application in the performance simulation study of the glass fiber filter media, which will provide a more specific and effective solution for the modeling and performance simulation study of the high-performance glass fiber filter media as well as efficiently accelerating the filter development.