Propargyl alcohol was coupled to 2,4-hexadiyne-1,6-diol (HDD) and crystallized in the process of ultraviolet irradiation-induced topochemical polymerization. The HDD polymer crystals were used as one component in the fabrication of organic photovoltaic cells, in combination with fullerene as the electron acceptor. The various structures of the produced photovoltaic cells included bilayer, trilayer, and bulk heterojunction structures. Their photovoltaic properties were analyzed in relation to crystal structure, electrochemical properties, and band structure of the HOD polydiacetylene polymers.