Molecular beacons (MBs) have shown fascinating applications in many biological fields. However, exploration of cost-effective, sensitive, stable and efficient MB for in situ live cell- based assay has still room for improvement. In this regards, we have developed a novel MB which bears a spherical graphite nanoparticle (GN) as a fluorescent quencher. The GN resulted in the high quenching efficiency, and the presence of GN enhanced the biological stability and transfection of the MB into the cells, thereby enabling the real-time survivin mRNA detection and quantification in the MCF-7 breast cancer cells. These results demonstrated that the advancement of the proposed MB containing a GN nanoquencher can be used as a robust molecular probe for genetic analysis in the cells.