Suzuki-Miyaura cross coupling (SMC) copolymerization of 3,8-dibromo-1,10-phenanthroline (PhenBr2) and 9,9-dioctylfluorene-2,7-diboronic acid (DOF[B(OH)2]2 was conducted aiming to synthesized an alternating copolymer composed of 1,10-phenanthroline-3,8-diyl and 9,9-dioctylfluorene-2,7-diyl units in a mixture of 1,2-dimethoxyethane and water using Pd(PPh3)4 and K2CO3 as catalysts at different temperatures. Side reactions were unexpectedly found to take place in the reactions at 100 °C where hydroxy and carbonyl groups appeared to be introduced probably to 1,10-phenanthroline units. Such reactions were more remarkable in the polymerization than in a model reaction leading to a triad molecule consisting of central 1,10-phenanthroline-3,8-diyl unit connected to two 9,9-dioctylfluorene-2-yl units, suggesting that a longer growing species has a role in such reactions. The extent of side reactions was higher with H2O than with D2O and was negligible with H218O. The polymer with structural defects showed photo absorbance and emission profiles and thermal properties which were remarkably different from those of the alternating copolymer without structural defects.