Separating the specific from the nonspecific bound single-strand DNA (ssDNA) is the most important step to improve the efficiency of selection procedure. However, most cell-SELEX protocols (where SELEX = systematic evolution of ligands by exponential enrichment) use simply washing only, which leads to incomplete separation. It is well-established that ssDNAs can be adsorbed on single-walled carbon nanotubes (SWCNTs). Based on this, herein, we developed a modified cell-SELEX approach termed "SWCNTs-assisted cell-SELEX". In our approach, SWCNTs are applied in the separation step, during which the unbound or the nonspecific ssDNAs are adsorbed onto SWCNTs, while the bound ssDNAs still remain on the cell surface, because of the stronger interaction between ssDNA and target. The cells can then be centrifuged to enrich the specifically binding aptamers. As a proof of concept, two nasopharyngeal carcinoma (NPC) cell lines-CNE2 cell and HONE cell-were used as the target cell and the negative cell, respectively. The result show that it takes only 6 cycles to enrich the aptamer pool through the SWCNTs-assisted cell-SELEX, which is much shorter than 15 cycles in the conventional cell-SELEX, thus improving the screening efficiency. Moreover, the achieved aptamers show high specificity and affinity with CNE2 cells, which are highly attractive for clinical diagnosis and biomedicine applications.