The microdomain structure of polystyrene-polymethylmethacrylate block copolymer (PS-b-PMMA) can be directed by a photochemically attached polymer surface layer. The photochemical attachment of the neutralization polymer on the silicon surface is a convenient and effective technique for interfacial energy control to provide the directed self-assembly of block copolymer. The perpendicular microdomain structure of PS-b-PMMA was formed on the polymer surface layer and the directed microdomain orientation of PS-b-PMMA was obtained on the polymer surface pattern.