In the process of removing cryoprotectants from cryopreserved blood, the theoretically optimal operating condition, which is based on the assumption that the distribution of red blood cells is uniform, is often used to reduce or even avoid the hypotonic damage to cells. However, due to the polydispersity of cells, the optimal condition is actually not reliable. In this study, based on the discrete concept developed in our previous work, the effect of the polydispersity on the recovery rate of cells in the dilution-filtration system was statistically investigated by assigning three random parameters, isotonic cell volume, cell surface area, and osmotically inactive cell volume, to cells in small units of blood. The results show that, due to the polydispersity, the real recovery rate deviates from the ideal value that is based on uniform distribution. The deviation significantly increases with the standard errors of cell parameters, and it can be also magnified by high cryoprotectant concentrations. Under the effect of polydispersity, the uniform distribution-based optimized blood or diluent flow rate is not perfect. In practice, one should adopt a more conservative blood or diluent flow rate so that the hypotonic damage to cells can be further reduced.