Merocyanines (MCs) are a versatile class of small-molecule dyes. Their optoelectronic properties are easily tunable by chemically controlling their donor−acceptor strength, and their structural properties can be tuned by simple side-chain substitution. This manuscript demonstrates a novel series of MCs featuring an indoline donor with varying hydrocarbon side-chain length (from 6 to 12 carbons) and a tertbutyl-thiazole acceptor, labeled InTBT. Bulk heterojunction organic photovoltaics are fabricated with a [6,6]-phenyl-C 61 -butyric acid methyl ester (PCBM) acceptor and characterized. Films composed of I8TBT:PCBM and I9TBT:PCBM produced the highest power conversion efficiency of 4.5%, which suggests that the morphology is optimized by controlling the side-chain length. Hierarchical structure formation in InTBT:PCBM films is studied using grazing incidence X-ray diffraction (GIXRD), small-angle neutron scattering (SANS), and atomic force microscopy (AFM). When mixed with PCBM, InTBTs with ≤8 side-chain carbons form pure crystalline domains, while InTBTs with ≥9 side-chain carbons mix well with PCBM. SANS demonstrates that increasing side-chain length increases the InTBT-rich domain size. In addition, a branched hexyl−dodecyl side-chain IHDTBT:PCBM film was studied and found to exhibit the worst-performance organic photovoltaic (OPV) device. The large-branched side chain inhibited mixing between IHDTBT and PCBM resulting in large segregated phases.