We use coarse-grained Langevin dynamics simulations of blends of generic conjugated polymers and acceptor molecules to show how architecture (e.g., side chains, backbone flexibility of oligomers) and the pair-wise interactions between the constituents of the blend affect morphology and phase transition. Alkyl side chains on the conjugated oligomer backbones shift the liquid crystal (LC) transition temperature from that of bare conjugated backbones and the direction of the shift depends on backbonebackbone interactions. Rigid backbones and constrained side chains cause a layer-by-layer morphology of conjugated polymers and amorphous acceptors, whereas flexible backbones and unconstrained side chains facilitate highly ordered acceptor arrangement. Strong backbonebackbone attraction shifts LC transition to higher temperatures than weak backbonebackbone attraction, and strong acceptoracceptor attraction increases acceptor aggregation. Pure macro-phase separated domains form when all pair-wise interactions in the blend are strongly attractive, whereas interconnected domains form at intermediate acceptoracceptor attraction and strong polymerpolymer attractions. (C) 2012 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2013