Flexible and electrically conductive polymer nanocomposite materials are gaining popularity as EMI shield materials. Herein, we report the successful fabrication of Thermoplastic polyurethane (TPU)/polybutylene adipate‐co‐terephthalate (PBAT)/dodecyl amine modified multi‐walled carbon nanotubes (MWCNT)‐based biodegradable polymer nanocomposite films employing solvent mixing and casting technique. The FESEM analysis of the cryofractured TPU/PBAT blend (containing 50 wt% of both the polymers) is found to be perfectly co‐continuous. Field emission scanning electron microscopy (FESEM), High‐resolution transmission electron microscopy (HRTEM) analysis followed by a selective dissolution test of polymer nanocomposites revealed that MAm nanofillers are mostly confined to the PBAT phase. The electrical percolation threshold is found to be between 3 and 5 wt% of dodecyl amine modified MWCNT loading as the electrical conductivity and EMI shielding efficiency are found to be shifting from 10⁻⁴ to 0.827 S/cm and −29.4 and −36 dB respectively as the nanofiller loading is increased from 3 to 5 wt% keeping the thickness of the polymer nanocomposite films constant at 0.8 mm.