The present invention provides a gene delivery system containing nanoparticles. In more detail, the present invention provides a gene delivery system containing (a) a nanomaterial (b) an oligonucleotide as an universal binding partner covalently linked to the surface of the nanomaterial and (c) a cargo comprising (i) a complementary oligonucleotide containing a nucleotide sequence complementary to the universal binding partner as a binding counter-partner, and (ii) an inhibitory molecule having a nucleotide sequence complementary to a target gene of interest to be inhibited or an inducible molecule having a nucleotide sequence of a target gene of interest to be expressed. The present invention is a gene delivery system capable of feasibly deliver aptamer, siRNA, shRNA, miRNA, ribozyme, DNAzyme, PNA or gene as well as antisense oligonucleotide into the cells. In addition, the present invention is more efficient than the commercially available gene transfer reagent in respect to the degree of knockdown of target protein expression.