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We have developed a “red blood cell (RBC)-photon simulator” to reveal optical propagation in prethrombus blood for various levels of RBC density and aggregation. The simulator investigates optical propagation in the prethrombus blood and will be applied to detect it noninvasively for thrombosis prevention in an earlier stage. In our simulator, Lambert-Beer's law is employed to simulate the absorption of RBCs with hemoglobin, while the Monte Carlo method is applied to simulate scattering through iterative calculations. One advantage of our simulator is that concentrations and distributions of RBCs can be arbitrarily chosen to exhibit the prethrombus, while conventional models cannot. Using the simulator, we found that various levels of RBC density and aggregation have different effects on the optical propagation of near-infrared response light in blood. The same different effects were acquired in in vitro experiments with 12 bovine blood samples, which were performed to evaluate the simulator. We measured RBC density using the clinical hematocrit index and RBC aggregation using activated whole blood clotting time. The experimental results correspond to the simulator results well. Therefore, we could show that our simulator exhibits the correct optical propagation for prethrombus blood and is applicable for the prethrombus detection using multiple detectors.