In this study, a novel route was proposed to fabricate entirely bio-based conductive nanocomposites with a low percolation threshold of conductivity (phi(c)) and enhanced crystallization and mechanical performances. In order to achieve this objective, poly(D-lactide)/poly(hydroxyalkanoate) (PDLA/PHA) nanocomposites with multi-walled carbon nanotubes (MWCNTs) and MWCNTs-g-PLLA (prepared via ring opening polymerization of L-lactide with grafting degree of 17%) were designed and fabricated. The grafting of PLLA facilitates the selective distribution of MWCNTs in the sole PDLA phase via interfacial stereocomplexation, which in combination with the volume exclusion effect of PHA leads to a lower value of phi(c) (phi(c) = 0.32 wt%) compared to that of the unmodified MWCNTs (phi(c) = 0.56 wt%). The localization of MWCNTs-g-PLLA in the PDLA phase was directly confirmed by scanning electron microscopy, transmission electron microscopy and supported by crystallization analysis by differential scanning calorimetry, X-ray diffraction, and polarizing optical microscopy. The presence of MWCNTs, in particular, the MWCNTs-g-PLLA significantly enhanced the crystallization rate of PDLA. Furthermore, MWCNTs networks in the nanocomposites were monitored by rheological analysis when the MWCNTs and MWCNTs-g-PLLA loading reached a critical value. The MWCNTs networks not only resulted in conductivity, but also strong reinforcement of the nanocomposites. For example, tensile strength of the PDLA/PHA blends increased from 32 to 50 MPa after the formation of MWCNTs network and leveled off at higher MWCNTs loadings. The bio-based conductive nanocomposites reported in this study exhibit significant potential in antistatic films and (semi-)conducting materials.