The purpose of this study is to propose a computer simulation method using particle method to analyze the formation and collapse of primary thrombus due to platelet aggregation in the blood flow. In the employed particle method, the blood region was discretized by particles that were assumed to have the characteristics of plasma and platelet. The MPS method that was developed for incompressible viscous flow was applied to the plasma flow. It was assumed that the platelets stochastically aggregate to the injured wall, and that the probability is expressed by hypothetic attractive force. In addition, spring force was introduced to express the deformation of the aggregated thrombus as a solid-like material. Two-dimensional simulations revealed that the proposed method reproduced initial thrombogenesis, growth of the thrombus, and its destruction. The blood flow rate influenced not only the amount of the aggregated platelets, but also the speed of the formation of a thrombus and the duration until a thrombus collapsed. These results demonstrated that the proposed method is useful to investigate the process of primary thrombogenesis which is regulated under the influence of fluid mechanical factors.