Formation of the platelet plug represents a primary response to the vessel wall injury, but may also result in vessel occlusion. The decrease of the local blood flow due to platelet thrombus formation may lead to serious complications, such as ischemic stroke and myocardial infarction. However, mechanisms responsible for regulation of thrombus dynamics are not clear. In order to get a deeper insight into the role of blood flow and platelet interactions in the formation of the primary platelet plug we developed a particle-based model of microvascular thrombosis using quasisteady flow approximation. In order to simulate thrombus dynamics at physiologically relevant timescales of several minutes, we took advantage of the supercomputer technologies. Our in silico analysis revealed the importance of platelet size heterogeneity for describing experimental data on microvascular thrombus formation. Thus, our model represents a useful tool for the supercomputeraided computational analysis of thrombus dynamics in the microvessels on physiologically relevant timescales.