Thermoelectric (TE) generation with solution‐processable conducting polymers offers substantial potential in low‐temperature energy harvesting based on high tunability in materials, processes, and form‐factors. However, manipulating the TE and charge transport properties accompanies structural and energetic disorders, restricting the enhancement of thermoelectric power factor (PF). Here, solution‐based strong acid–base treatment techniques are introduced to modulate the doping level of poly(3,4‐ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) thin films with preserving its molecular orientation, enabling to achieve a remarkably high PF of 534.5 µW m−1 K−2. Interestingly, theoretical modeling suggested that further de‐doping can increase the PF beyond the experimental value. However, it is impossible to reach this value experimentally, even without any degradation of PEDOT crystallinity. Uncovering the underlying reason for the limitation, an analysis of the relationship among the microstructure–thermoelectric performance–charge transport property revealed that inter‐domain connectivity via tie‐chains and the resultant percolation for transport are crucial factors in achieving high TE performance, as in charge transport. It is believed that the methods and fundamental understandings in this work would contribute to the exploitation of conducting polymer‐based low‐temperature energy harvesting.