The achievement of functional nanomodules for subcellular label-free measurement has long been pursued in order to fully understand cellular functions. Here, a compact label-free nanosensor based on a fiber taper and zinc oxide nanogratings is designed and applied for the early monitoring of apoptosis in individual living cells. Because of its nanoscale dimensions, mechanical flexibility, and minimal cytotoxicity to cells, the sensing module can be loaded in cells for long term in situ tracking with high sensitivity. A gradual increase in the nuclear refractive index during the apoptosis process is observed, revealing the increase in molecular density and the decrease in cell volume. The strategy used in our study not only contributes to the understanding of internal environmental variations during cellular apoptosis but also provides a new platform for nonfluorescent fiber devices for investigation of cellular events and understanding fundamental cell biochemical engineering.