Antigen CD133 is a glycoprotein present on the surface of cancer stem cells (CSCs), which is a key molecule to regulate the fate of stem cells and a functional marker of stem cells. Herein, a novel fluorescence turn-on nano-aptamer sensor for quantifying CD133 was designed using hybridization between CD133-targeted aptamers and partially complementary paired RNA (ssRNA), which were modified on the surface of quantum dots (QDs) and gold nanoparticles (AuNPs), respectively. Owing to the hybridization of aptamers and ssRNA, the distance between QDs and AuNPs was shortened, which caused fluorescence resonance energy transfer (FRET) between them, and the florescence of QDs was quenched by AuNPs. When CD133 competitively replaced ssRNA and was bound to aptamers, AuNPs-ssRNA could be released, which led to a recovery of fluorescent signals of QDs. The increase in the relative value of fluorescence intensity was investigated to linearly correlate with the CD133 concentration in the range of 0-1.539 μM, and the detection limit was 6.99 nM. In confocal images of A549 cells, the CD133 aptamer sensor was further proved applicable in lung cancer cell samples with specificity, precision, and accuracy. Compared with complicated methods, this study provided a fresh approach to develop a highly sensitive and selective detection sensor for CSC markers.