Materials based on poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) can be potentially employed as flexible thermoelectric generators (TEGs) to capture waste heat and generate electrical energy. Among various methods, secondary doping is an effective way to modulate its thermoelectric (TE) performance. Different from conventional measures such as dropping, soaking, and steam fumigation, strong shear is integrated with the doping process and termed high-velocity non-solvent turbulent secondary doping (HNTD). We systematically investigate the transformation of PEDOT:PSS during this procedure and the formation mechanism of its highly conductive pathway. It is illustrated that PEDOT:PSS experiences PSS swelling, the phase separation of PEDOT from PSS, the removal of isolated PSS, and the evolution of PEDOT to a linear conformation. These evolutions contribute to the substantial elevation of electrical conductivity (σ). Furthermore, by employing continuous single-walled carbon nanotube (SWCNT) networks as structural units, highly conductive flexible PEDOT:PSS/SWCNT TE thin films could be prepared without sacrificing the Seebeck coefficient ( S ). Additionally, the effect of HNTD and direct addition method on TE properties of composite films is also compared. Finally, the PEDOT:PSS composite film with 40 wt % SWCNTs by the HNTD method exhibits the maximized power factor (PF) of 501.31 ± 19.23 μW m -1 K -2 with σ of 4717.8 ± 41.51 S cm -1 and S of 32.6 ± 0.13 μV K -1 at room temperature. It is worth mentioning that the σ value 4717.8 ± 41.51 S cm -1 is the highest among the composites based on commercial carbon fillers and organic semiconductors. Finally, a 6-leg TEGs prototype is assembled and illustrates an output power of 4.416 μW under a temperature difference (Δ T ) of 58 K. It is thought that such a strategy may provide some guidelines for manufacturing PEDOT:PSS-based functional materials.