Mucin 1 (MUC1) is a glycoprotein expressed on most epithelial cell surfaces, which has been confirmed as a useful biomarker for the diagnosis of early cancers. In this paper, we report an aptamer-based, quantitative detection protocol for MUC1 using a 3-component DNA hybridization system with quantum dot (QD)-labeling: in the absence of MUC1 peptides, strong fluorescence is observed upon mixing the three specially designed DNA strands (quencher, QD-labeled reporter, and the MUC1 aptamer stem); in the presence of MUC1 peptides, a successive decrease in fluorescence intensity is detected since the MUC1 peptide binds to the aptamer strand in such a way to allow the quencher and fluorescence reporter to be brought into close proximity (which leads to the occurrence of fluorescence resonance energy transfer, FRET, between the quencher and QD). The detection limit for MUC1 with this novel approach is in the nanomolar (nM) level, and a linear response can be established for the approximate range found in blood serum. This study also provided further insight into the aptamer/analyte binding site/mode for MUC1, which augments the possibility of improving this detection methodology for the early diagnosis of different types of epithelial cancers of large populations.