To investigate the influence of CuPc-(SO3H)2 doping methods on the thermoelectric properties of polyaniline (PANi), in this work, HPANi (in situ polymerization of aniline doped by HCl), HPANi/Cu (HPANi directly mixed with CuPc-(SO3H)2), CuPANi (in situ polymerization of aniline doped by CuPc-(SO3H)2) and CuHPANi (in situ polymerization of aniline co-doped by HCl and CuPc-(SO3H)2) were synthesized. CuPc-(SO3H)2 impedes carrier transport of HPANi/Cu, CuPANi and CuHPANi, however, their Seebeck coefficients are surprisingly enhanced. The Seebeck coefficients of HPANi/Cu (54.36 μ V K−1) and CuHPANi (20.97 μ V K−1) are more than 5.2 times and twice that of HPANi (10.40 μ V K−1), respectively. Interestingly, the Seebeck coefficient of CuPANi is 30.92 μ V K−1 at 300 K, while it becomes negative above 333 K and reaches −392.80 μ V K−1 at 363 K. The structural characteristics were discussed to further reveal the thermoelectric performance differences among all the samples.