In this work, a study was carried out to compare the filtering and hydrodynamic properties of granular filters with solid spherical granules and spherical granules with modifications in the form of micropores. We used the discrete element method (DEM) to construct the geometry of the filters. Models of granular filters with spherical granules with diameters of 3, 4, and 5 mm, and with porosity values of 0.439, 0.466, and 0.477, respectively, were created. The results of the numerical simulation are in good agreement with the experimental data of other authors. We created models of granular filters containing micropores with different porosity values (0.158−0.366) in order to study the micropores’ effect on the aerosol motion. The study showed that micropores contribute to a decrease in hydrodynamic resistance and an increase in particle deposition efficiency. There is also a maximum limiting value of the granule microporosity for a given aerosol particle diameter when a further increase in microporosity leads to a decrease in the deposition efficiency.