Compared to the great achievements in enhancing thermoelectric (TE) performance, little attention is paid to the mechanical (ME) performance of polymer composites although it is a prerequisite for practical applications. However, how to improve a trade-off between TE and ME performance is a great challenge, as the increase in ME performance is always along with the decrease in TE performance and vice versa. Herein, an enhanced trade-off is realized for ionic liquid (IL)-modulated flexible poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS)/ single-walled carbon nanotube (SWCNT)/polycarbonate (PC) composites. It shows a maximum power factor value of 8.5 ± 2.1 μW m−1 K−2 and a strong mechanical robustness is also achieved for the composite with a fracture strength of 43.4 ± 5.4 MPa and a tensile modulus of 3.8 ± 0.4 GPa. The TE and ME performances are superior to other thermoplastics-based TE composites, and even comparable to some conducting polymers and their composites. The high electrical conductivity of PEDOT:PSS/SWCNT and their strong interfacial interaction with PC are responsible for the enhanced trade-off between ME and TE performances. This work provides a new avenue to endow polymer composites with high TE and ME performances simultaneously and will promote their versatile TE applications.