Glassy matter, as subjected to high shear rates, exhibit shear thinning : i.e., the viscosity diminishes with increasing shear rate. Meanwhile one prominent difference between the transport in micropores and that in macroscale is the (relatively) larger roughness observed inside micropores. As the pore size decreases, the surface-to-volume ratio increases and therefore, surface roughness will greatly affect the transport in micropores. By treating the glass as a shear-thinning matter and using the rate-dependent model together with the boundary perturbation method, we can analytically obtain the transport results up to the second order.