The effect of fluid flow on protein patterning and the stability of the adsorbed protein array templated by polystyrene-block-poly(methyl methacrylate) (PS-b-PMMA) has been investigated. Protein nanoarrays can be formed on a PS-b-PMMA copolymer surface by physisorption and rinsing with an open flow. The protein arrays inherit the original hexagonal pattern generated by the phase separation of PS-b-PMMA with the proteins only residing on the PS domains. Subsequent analysis of the protein array stability tinder confined flow field reveals that the array integrity is strongly dependent on the now velocity and the duration time. The interplay between the intermolecular forces and the hydrodynamic shear force has been discussed in detail. A simplified model has been proposed to explain the site-selective adsorption and protein migration under the shear of fluid flow. This study provides valuable information on the fort-nation mechanism and stability of physisorbed protein nanopatterns underconditions concerning biosensing applications. It also represents an explorative study of protein adsorption under hydrodynamic flow conditions, which may assist in better designs of fluidic devices relevant to protein studies.