Small molecule additives have been shown to increase the device efficiency of conjugated polymer (donor) and fullerene derivative (acceptor) based organic solar cells by modifying the morphology of the device active layer. In this paper we conduct a systematic study of how additives affect the donoracceptor morphology using molecular dynamics simulations of blends of thiophene-based oligomers, mimicking poly(3-dodecylthiophene) (P3DDT) or poly(2,2 0 :5 0 ,2"-3,3"-didocyl-terthiophene) (PTTT), and fullerene derivatives with additives of varying length and chemical functionalization, mimicking experimentally used additives like methyl ester additives, diiodooctane, and alkanedithiols. We find that functionalization of additives with end groups that are attracted to acceptor molecules are necessary to induce increased donor-acceptor macrophase separation. In blends where acceptors intercalate between oligomer alkyl side chains, functionalized additives decrease acceptor intercalation. Functionalized additives with shorter alkyl segments increase acceptor macrophase separation more than additives with same chemical functionalization but longer alkyl segments.Recent studies have suggested that additives, such as CN, facilitate polymer aggregation in solution, 6,13,14 creating many nucleation sites and leading to the formation of a fibril polymer network with the [6,6]-phenyl-C 61 -butyric acid methyl ester (PCBM) filling the spaces in that polymer network. 13 For PBDTTPD (poly(di(2-ethylhexyloxy)benzo[1,2-b:4, 5b 0 ]dithiophene-co-octylthieno [3,4-c]pyrrole-4,6-dione):PC 70 BM blends with highly phase segregated as-cast morphologies, domain sizes shrink with additive-induced polymer nucleation creating a more interconnected morphology with high interfacial area that is thought to be better for device efficiency than large phase separated domains. 13 When the as-cast morphology is intermixed, additive-induced polymer nucleation allows for Additional Supporting Information may be found in the online version of this article.