In the study, a series of polypyrrole (PPy) samples were prepared by a method of template synthesis at different indigo carmine (IC) concentrations while keeping the amount of pyrrole and FeCl3 as well as the reaction conditions unchanged. Effects of IC concentration (M-IC) on the morphology, conductivity and microwave absorbing behavior of the obtained PPy products were investigated. The results showed that the morphology of PPy transformed from granular flocking to rods and then to spiral rods as M-IC increased from 0.05 to 7.50 mM, and the morphology transformation mechanism of PPy was attributed to the structural transformation of IC micelles caused by the change of M-IC. The conductivity of PPy was also found to be influenced by M-IC. Further investigation indicated that the spiral rod-shaped PPy (S-5) showed obviously superior microwave absorbing behavior compared with that of the granular flocking shaped PPy or that of the rod-shaped PPy, which was attributed to the benefits of its spiral structure and the comparably higher dielectric loss resulted from its lower conductivity.