Co-doped polyaniline (PANI) was synthesized in microemulsion by hydrochloric acid (HCl) and dodecylbenzene sulfonate (SDBS) then thermal treated in air at 160 and 200 °C for 0.5 h, respectively. The changes of structure, thermal stability, micromorphology and electrical conductivity after thermal treatment were studied by Fourier transformed infrared (FT-IR), Thermogravimetric analysis (TGA), X-ray diffraction (XRD), scanning electron microscope (SEM) and four-probe technique. It was found that the conductivity of PANI decreased about 50% after thermal treated at 160 °C, and droped by 2 orders of magnitude at 200 °C. This may be explained by that only a fraction of total mass of HCl losses during thermal treatment at 160 °C, but after heating at 200 °C, the dedoping of dodecylbenzene sulfonic acid (DBSA) along with cross-linking, chain scission and oxygen incorporation in a form of carbonyl groups take place, resulting in destruction of crystal structure, decrease of the emeraldine sequence, lower thermal stability and heterogeneous micromorphology.