The dissipative particle dynamic (DPD) method is applied to simulate the DNA separation process based on a mechanism developed earlier by other authors, who demonstrated a micro-device for separating DNA molecules (>2kbp) through an entropic trapping mechanism. The DPD is used to model the process because it is intrinsic to modeling hydrodynamic interactions, which is lacking in some earlier works. We use the worm-like chain model to represent DNA molecule and Lennard–Jones potential at mesoscopic level to avoid phantom collision between the chain beads. Our simulations show that longer DNA strands do move faster than shorter ones, as observed in available experimental data. We also confirm that the delayed entrance is the cause of entropic trapping. Contrary to some earlier reported data, we found that the corner trapping is not a contributor to DNA separation.