Non-invasive living cell microscopy in real time is essential for a wide variety of biomedical research. Here, we present a subcellular refractive index imaging technique for living cells based on a graphene biosensor system. Owing to the optical reflectivity differences of graphene to s- and p-polarizations, a 45° generalized-cylindrical-vector-polarized laser beam is employed to demodulate the reflected cylindrical vector beam for differential detecting. Benefitting from the vector beam-enabled common-path graphene biosensor, the imaging spatial resolution and refractive index sensitivity are noticeably improved. Subcellular refractive index mapping of live human colonic cancer cells is perfectly achieved without inducing any cell damage. Furthermore, real-time monitoring of an individual cell is also performed with the disassembly of the cell nucleolus clearly observed. This technique would be a promising tool for the study of living cell morphology, kinetics, and pathology, and for other biomedical research.