Aim of this article was to investigate the effect of grain boundaries on the interfacial properties of bi-crystalline graphene/polyethylene based nanocomposites. Molecular dynamics based atomistic simulations were performed in conjunction with the reactive force field parameters to capture atomic interactions within graphene and polyethylene atoms, whereas non-bonded interactions were considered for the interfacial properties. Atoms at the higher energy state in bi-crystalline graphene helps in improving the interaction at the nanocomposite interphase. Geometrical imperfections such as wrinkles and ripples helps the bi-crystalline graphene in increasing the number of adhesion points between the nanofiller and matrix, which eventually improves the strength and toughness of nanocomposite. These outcomes will help in opening new opportunities for defective nanofillers in the development of nanocomposites for future applications.