Molecular dynamics simulations are used to study the influence of functionalized substrates on the orientation of poly(3-hexylthiophene) (P3HT) nanocrystallites, which in turn plays a critical role in P3HT-based transistor performance. The effects of alkyl-trichlorosilane self-assembled monolayer packing density, packing order, and end-group functionality are independently investigated. Across these factors, the potential energy surface presented by the substrate to the P3HT molecules is determined to be the main driver of P3HT ordering. Surprisingly, disordered substrates with a smoothly varying potential energy landscape are found to encourage edge-on P3HT orientation, while highly ordered substrates have undesirable potential energy wells that reduce the edge-on orientation of P3HT because of substrate-side-chain interactions.