Surface modification of inorganic nanoparticles (NPs) is extremely necessary for biomedical applications. However, the processes of conjugating ligands to NPs surface are complicated with low yield. In this study, a hydrophilic shell with excellent biocompatibility was successfully constructed on individual gold NPs or gold nanorods (NRs) by encapsulating NPs or NRs in graphene oxide (GO) nanosheets through electrostatic self-assembly. This versatile and facile approach remarkably decreased the cytotoxicity of gold NPs or NRs capping with surfactant cetyltrimethylammonium bromide (CTAB) and provided abundant functional groups on NPs surface for further linkage of polyethylenimine (PEI). The PEI-functionalized GO-encapsulating gold NPs (GOPEI-AuNPs) were applied to delivery DNA into HeLa cells as a novel gene vector. It exhibited high transfection efficiency of 65% while retaining 90% viability of HeLa cells. The efficiency was comparable to commercialized PEI 25 kDa with the cytotoxicity much less than PEI. Moreover, the results on transfection efficiency was higher than PEI-functionalized GO, which can be attributed to the small size of NPs/DNA complex (150 nm at the optimal w/w ratio) and the spherical structure facilitating the cellular uptake. Our work paves the way for future studies focusing on GO-encapsulating, NP-based nanovectors.