A series of linear and star-shaped pi-conjugated oligomer hybrids (2-5) composed of an oligoyne core, ranging from 1,3-butadiyne to 1,3,5,7,9,11-dodecahexayne, and fullerenyl end-capping groups has been synthesized and studied. The molecular structures of these fullerene-oligoyne hybrids were assembled through three key reactions: Pd-catalyzed cross-coupling, Cu-catalyzed oxidative homocoupling, and an in situ alkynylation reaction on [60]fullerene. The properties of these compounds were investigated by UV-vis spectroscopy, differential scanning calorimetry (DSC), and atomic force microscopy (AFM) with the purpose of understanding the thermal reactivity arising from the oligoyne moieties as well as the morphological properties on surface. Our study shows that these fullerene-oligoyne hybrids tend to aggregate in different morphologies, including nanospheres, nanoflakes, and continuous thin films, while the morphological properties appear to be subject to the influence of molecular factors such as oligomer chain length, solubilizing alkylphenyl groups, and the thermal reactivity of the oligoyne unit. The correlation between molecular property and interfacial aggregation behavior evinced by these fullerene-oligoyne hybrids suggests a viable approach to exert bottom-up control over the structures and properties of fullerene based nanomaterials.