A new type π-conjugated poly(2,5-didodecyloxy-1,4-diethynyl-phenylene-alt-2-methyl-4,6-pyrimidine) was prepared by Sonogashira polycondensation. A fuel cell catalyst is prepared by depositing platinum particles on carbon nanotubes which was modified with poly(2,5-didodecyloxy-1,4-diethynyl-phenylene-alt-2-methyl-4,6-pyrimidine) and the previously reported poly(2,5-didodecyloxy-1,4-diethynyl-phenylene-alt-2-amino-4,6-pyrimidine). After comparing the two catalysts, it is found that active sites and catalytic performance of catalysts are significantly influenced by the copolymer on the carbon nanotubes which was the catalysis carrier. The electrochemically active surface area (ECSA) of catalysts containing poly(2,5-didodecyloxy-1,4-diethynyl-phenylene-alt-2-methyl-4,6-pyrimidine) was calculated to be 25.5 m2 g-1, which is higher than the ECSA of the poly(2,5-didodecyloxy-1,4-diethynyl-phenylene-alt-2-amino-4,6-pyrimidine) containing catalyst (18.2 m2 g-1). And the first polymer provides better methanol oxidizability and durability than second polymer for catalyst.