A thienylsilane molecular layer is self-assembled onto vertically aligned ZnO nanowire templates for promoting in situ electrochemical polymerization of P3HT. The silane functionalization on ZnO surface is investigated using x-ray photoelectron spectroscopy and water contact angle measurements. The silane-based surface modified layer acts as a favorable nucleation site for electrochemical polymerization. We find that the oxidation potential for electrochemical polymerization is obviously decreased compared to that without a surface modifier. The UV-visible absorption in the ZnO nanowire/P3HT film with thienylsilane molecular layer is much stronger than that without surface modification.