A series of two-monomer-connected-precursor polymerization-based polypyrrole (PPy) films was prepared by modulating the film morphologies by varying the diacid linkers. During the polymerization, ionically crosslinked and self-doped PPy films were obtained. The structure obtained using 1,5-napthalenedisulfonic acid (PPy-Nap) with a fused aromatic linker exhibited a higher electrical conductivity (~78 S cm−1) than that (6.7 S cm−1) without a linker (PPy-ref). This large improvement in the morphology significantly increased the electrical conductivity while maintaining the Seebeck coefficient, yielding enhanced thermoelectric properties, compared with those of the other PPy samples. The theoretical analysis based on the Kang–Snyder model suggested that the highly ordered conductive domains significantly decreased the transport barrier and increased the carrier mobility, improving the power factor without decreasing the Seebeck coefficient.