Gold nanorods (GNRs) have aroused the extensive interest of many researchers in recent years due to their unique physicochemical properties. However, the toxic cetyltrimethylammonium bromide (CTAB) is often introduced into the process of synthesizing GNRs, which hinders the wide-range applications of GNRs in clinical practice. To reduce the toxicity, the CTAB molecules coated on the surface of GNRs should be replaced by nontoxic and biocompatible agents such as phospholipid. Thus the component and morphology of the mixed coating agents on the surface of GNRs affect the physicochemical properties of GNRs. To study the morphology and properties of the coated GNRs at a molecular level, we investigate the self-assembly of GNRs, CTAB, and dimyristoyl phosphatidylcholine (DMPC) by using solvent-free dissipative particle dynamics simulations. Our results show that the morphology of the assembled complex mainly depends on the CTAB/DMPC molar ratio, while neither of the interaction strength between GNRs and the coating agents nor the diameter of GNRs has significant effect on the morphology. At a certain combination of GNRs-coating agent interaction strength with GNRs diameter, the mixture of CTAB and DMPC on the surface of GNRs undergoes a gradual change in morphology as the CTAB/DMPC molar ratio increases, including the forming of intact bilayer membrane, cracked bilayer membrane, long patches of micelles, and short wormlike micelles winding GNRs in spiral shape. The morphology of intact bilayer membrane verifies the experimental guess, while the other three morphologies are brand-new discoveries. We also find that when the GNR’s diameter becomes smaller, or the CTAB/DMPC molar ratio is larger, or the interaction strength is greater, the agents cap the ends of GNRs, meanwhile the membrane thickness becomes thinner. The multiple morphologies of the assembled complexes can be qualitatively explained by the shape energy of a membrane adsorbed on a solid surface. When the surface tension of the membrane (which is proportional to the spontaneous curvature of the membrane) exceeds a critical value (which is equal to the adhesion energy density of the membrane), the membrane dissociates from the solid surface and its shape changes. The change trend is related to the spontaneous curvature of the free membrane. As a result of the synergy and competition among the inherent curvatures of GNRs, the spontaneous curvature of CTAB/DMPC membrane or micelle, as well as the adhesion energy, various interesting morphologies are produced. Our simulations and analyses directly characterize the morphological structures of CTAB and lipid coated GNRs, which allow us to in depth understand the self-assembling behaviors of GNRs at a molecular level. This is also conductive to achieving the controlled assemblies of GNRs.