Graphene-based nano-technology is the future of biomedical devices including biosensors and, hence, it is essential to unravel the interaction of graphene oxide (GO) with cellular membrane. Here, the structural reorganization of lipid molecules, which are the building blocks of a cellular membrane, has been demonstrated in presence of GO flakes. The membrane is mimicked by forming a stack of lipid bilayers of zwitterionic phospholipid 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and its structures have been probed by X-ray reflectivity and grazing incidence X-ray diffraction techniques. Lipid-GO composites have exhibited two sets of lamellar diffraction peaks illustrating GO-rich micro-domains in the matrix of phospholipid bilayers (GO-poor phase). In these domains, the GO flakes are observed to penetrate into hydrophobic core of the bilayer altering the thickness along with the overall electron density profile of the lipid layer. The GO-poor bilayer is closely related to the phase formed by pristine lipid molecules. The lattice parameters of a body-centred rectangular unit cell formed by chains of saturated phospholipids are found to be modified in presence of GO with a significant effect on molecular tilt. The structural description of GO-membrane interaction may pave the way of discerning the physical behaviour of the composites. © 2020 Elsevier B.V.