Using molecular dynamics simulations, we theoretically investigate the molecular orientation of poly(3-hexylthiophene) (P3HT) on hydrophobic and hydrophilic self-assembled monolayers (SAMs). In particular, we study the effects of roughness at the SAM surfaces on the molecular orientation of P3HT molecules put on the surface. The energetically preferable molecular orientation does not change by the roughness we introduced. The roughness induces more frequent transition between the edge-on and face-on orientations, when a small number of P3HT molecules are put on the hydrophobic SAM.