It is known for hydrophobic small molecules and proteins to be strongly adsorbed on the surface of polydimethylsiloxane (PDMS) based microdevices. However, no systematic studies have addressed issues related to the sorption of nanoparticles (NPs) on PDMS surfaces. The authors have used carboxylate-modified polystyrene nanoparticles (PS NPs), with sizes of < 100 nm and prepared in different curing agent ratios, to study their sorption by native PDMS of different brands. It is found that both dynamic coating with sodium dodecyl sulfate and sol-gel modification can relieve the sorption issues, but only the co-treatment with both species gives satisfactory results in terms of suppressing bulk absorption. This combined coating strategy was further testified by an on-chip separation of a mixture of PS NPs (of 20 nm, 50 nm and 500 nm average diameter) based on a linear node array with enhanced mixing and diffusion-biased recovery of smaller nanoparticles. Instead of changing device design, optimal parameters for nano-separation can be achieved by changing the flow rate between a pair of syringe pumps. A more than 10-fold enrichment of 20 nm NPs was obtained when analyzing a mixture of nanoparticles. Since PDMS is still the preferred choice as a microfluidic substrate, this combined coating strategy is perceived to be highly beneficial in on-chip nano-separation and nanosynthesis using PDMS based microdevices.