Through dissipative particle dynamics method, a coarse-grained model of polypeptide was established, and the effects of flow field strength, molecular concentration, molecular chain length, and solvent properties on the flow behavior of peptides driven by pressure in microchannels were studied. It is found that the polypeptide solution exhibits shear thinning behavior, with the increase of the flow field strength, the relative concentration near the wall decreases; with the increase of the solution concentration, the flow velocity at the center of the channel increases, and the tendency of the polypeptide to move away from the wall increases; with the increase of the chain length and solvent solubility, the migration tendency of the polypeptide from the wall to the center of the channel is enhanced. Through the analysis of the flow field and relative concentration distribution under different conditions, it is suggested that different conditions have important influence on the flow and migration characteristics of polypeptide microchannels, and the flow and migration mechanism of polypeptides under different conditions was explained from the perspectives of hydrodynamics and rheology.