In this paper, epoxy nanocomposites were developed via polythiophene–carbon nanotube with different loadings of 0–1.0 wt%. Polythiophene–carbon nanotube (PTh–CNT) hybrids produced using in situ chemical polymerization method and the microstructures, morphology and properties of the PTh–CNT hybrids and epoxy nanocomposites were studied using Fourier-transform infrared (FTIR), scanning electron microscopy (SEM), transition electron microscopy (TEM), mechanical (tensile and flexural properties), electrical, dynamic mechanical thermal analysis (DMTA) and thermogravimetric techniques (TGA). Mechanical analysis demonstrated that nanocomposites containing 0.5% PTh–CNT hybrids exhibited the highest properties among all nanocomposites and showed 78% and 51% increment of Young’s modulus and strength. The fracture analysis of samples and extent of fillers dispersion were visualized by SEM and demonstrated that dispersion of hybrids within epoxy matrix related to the hybrid nature (PTh–CNT ratio) and its concentration that are the key factors affected final properties of nanocomposites. DMA thermograms represented higher modulus for all epoxy/PTh–CNT nanocomposites systems as compared to epoxy/CNT and the pristine epoxy. Electrical conductivity measurements showed that conductivity of epoxy filled nanocomposites increased up 10−1 S cm−1 for epoxy/PTh–CNT nanocomposites. In addition, epoxy/PTh–CNT nanocomposites were also compared to pure epoxy and epoxy/CNT nanocomposites and showed higher thermal stability. The PTh–CNT particles enhanced electrical, thermal and fracture toughness of nanocomposites, confirming the synergistic effect of PTh–CNT as multifunctional filler.