This study examined the effect of a chemically nanostructured surface of cylinder forming poly(styrene-b-methyl methacrylate) (PS-b-PMMA) and poly(styrene-b-4vinyl pyridine) (PS-b-P4VP) block copolymer gate dielectrics on the performance of the bottom gate pentacene organic thin film transistor (OTFT). The field effect mobility of pentacene is affected mainly by the chemical properties of the top skin of a block copolymer layer. In the case of PS-b-PMMA with cylindrical PMMA microdomains that are located very closely at the block copolymer-pentacene interface because the surface energy of PMMA is similar to that of PS, the field effect mobility in general corresponds to the area averaged value of the two mobilities with the pure PS and PMMA layer. On the other hand, PS-b-P4VP copolymer results in a similar field effect mobility to that of the pure PS layer because the cylindrical P4VP microdomains are embedded in the PS matrix of which the surface energy is much lower than that of P4VP. The orientation of the cylindrical PMMA microdomains with respect to the surface also affects the field effect mobility, where the PMMA microdomains are aligned perpendicular to the surface, gave rise to a mobility approximately 50% higher than those parallel to the surface. The composite model with parallel and series resistance units offers qualitative understanding of these results.