Using molecular dynamics simulations we study blends of oligomers of 2,5-bis(3-alkylthiophen-2-yl)thieno [3,2-b]thiophene, BTTT, and fullerene derivative based acceptors to understand the role of oligomer length and alkyl side chain (SC) length on the morphology of their blends. We use a validated coarse-grained model of BTTT and fullerene derivatives presented in recent work along with direct comparison of morphology between simulations and experiments. In this article, we predict computationally that short alkyl SCs (6 alkyl groups) decrease the propensity of fullerene derivative acceptors to intercalate between SCs on the BTTT backbone compared to longer alkyl SCs (9 or 12 alkyl groups), and as a result increase acceptor aggregation. The decreasing acceptor intercalation and increasing acceptor aggregation do not significantly impact the positional or orientational order of the BTTT backbones. However, the BTTT oligomer backbones order better with increasing SC length in both neat systems and in blends, with the blends exhibiting higher positional order than neat systems. While these qualitative trends are similar both in 2mer blends and 4mer blends, we see a larger extent of acceptor intercalation and as a result, smaller acceptor cluster sizes in the 4mer blends. V C 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016, 54, 89-97