This study examined the functional morphology of the trace fossil Paleodictyon in terms of computational fluid dynamics. The modern specimens show a unique morphology that is composed of a hexagonal mesh structure, vertical shafts opening to the seafloor, and a shield-like mound on the seafloor. The traces of the vertical shafts were also preserved in some fossil examples. To explain their characteristic morphology, a “passive ventilation” hypothesis has been proposed suggesting that their function was to ventilate their burrows with bottom currents, which supply both oxygenated water and food. However, this hypothesis has not yet been verified. This study conducted numerical experiments to understand the functions of the structures created by this ichnofossil by using a model of computational fluid dynamics with the 3D geometry of Paleodictyon and estimating the efficiency of the ventilation in burrows. As a result, it was observed that seawater flowed in the vertical shafts in the marginal area of the mound, and flowed out from the shafts located on the top of the mound, flowing through the mesh structure. This ventilation was observed only in the case that Paleodictyon had a shield-like mound. The ventilation rate rapidly increased as the bottom current velocity increased. In contrast, the rate also increased with the height of the shield-like mounds, whereas it once dropped after the minor peak at 4 mm in height, which corresponds to the value measured in the modern specimens. This coincidence may imply that the height of the mound observed in modern specimens resulted from the optimization in balancing between the efficiency of ventilation and physical stability against erosion. Full exchange of water in the mesh structure by ventilation took less than a few minutes at this mound height, which is presumably sufficient for the ability of Paleodictyon producers.