Directional dipole-dipole interaction mediated antiparallel dimerization of merocyanine dye (MD) has been explored for maneuvering supramolecular assembly of MD-conjugated flexible macromolecules leading to a cross-linked nanogel. The MD-functionalized copolymer was synthesized by a newly developed organocatalytic transesterification strategy for postpolymerization functionalization of poly(pentafluorophenyl acrylate) (polyPFPA)-based reactive copolymer. Presence of ∼35% pendant MD attached to a coil-like polymer chain leads to spontaneous formation of highly emitting cross-linked nanogel with efficient container property and appreciable stability in toluene owing to strong dimerization propensity among the MD. Considering the significance of MD in the context of nonlinear optics and photovoltaics, these results not only enrich the toolbox for engineering macromolecular assembly, but also open up new possibilities for future organic materials.