Polypyrrole(PPy) nanorod networks with a high electrical conductivity of 40 S cm–1 have been obtained in a high yield by employing an ion association of heparin–methylene blue as a new morphology-directing agent. The polypyrrole nanorod networks are mixed with different content of carbon nanoparticles to make PPy nanorod networks/carbon nanoparticles(PPy/C) counter electrodes. It is found that the PPy/C composite with 10% carbon content shows a lower charge transfer resistance and better catalytic performance for the reduction of I3–, compared with the pristine PPy and carbon electrodes. The better catalytic performance is attributed to the interaction of the superior electrocatalytic activity of the unique polypyrrole nanorod networks and the carbon nanoparticles, which can accelerate triiodide reduction and electron transfer in the electrode. Under standard AM 1.5 sunlight illumination, the dye-sensitized solar cell based on the PPy/C composite with 10% carbon content as the counter electrode demonstrates a high efficiency of 7.2%, which is much higher than that of pristine PPy and carbon electrode-based DSCs and comparable to that of the thermal decomposed Pt-based DSC.