Tissue characterization using ultrasound (US) scattering allows extraction of relevant cellular biophysical information noninvasively. Characterization of the level of red blood cell (RBC) aggregation is one of the proposed application. In the current paper, it is hypothesized that the microstructure of the RBCs is a main determinant of the US backscattered power. A simulation model was developed to study the effect of various RBC configurations on the backscattered power. It is an iterative dynamical model that considers the effect of the adhesive and repulsive forces between RBCs, and the effect of the flow. The method is shown to be efficient to model polydispersity in size, shape, and orientation of the aggregates due to the flow, and to relate these variations to the US backscattering properties. Three levels of aggregability at shear rates varying between 0.05 and 10s−1 were modeled at 40% hematocrit. The simulated backscattered power increased with a decrease in the shear rate or an increase in the RBC aggregability. Angular dependence of the backscattered power was observed. It is the first attempt to model the US power backscattered by RBC aggregates polydisperse in size and shape due to the shearing of the flow.