The evolution of nanotechnology gives impetus to the regenerative medicine growth, which has led to the great research interest in studying the interaction between stem cells and nanoparticles (NPs). The study of intracellular fate of NPs is generally consisted of two aspects: the dynamic tracking of NPs (NPs localization and transportation) and the quantification of intracellular NPs content. However, there is a lack of tools that could satisfy both requirements at the same time. In this work, Prussian blue nanoparticles (PBNPs) were chosen as model probes to study the fate of NPs in living cells. By combining the live cell imaging system with proposed quantification method (pixel-based colorimetry method), we realized a long-term monitoring and dynamic quantitation of PBNPs in living stem cells at the single-cell level. NPs fate tracking and quantitative analysis have visualized the asymmetrical inheritance of PBNPs in two daughter cells during mitosis and the reduction of PBNPs during interphase, which is mainly attributed by lysosomal digestion. As demonstrated by our results, we identified three factors that contributed to the PBNPs load change within one cell cycle: asymmetric cell inheritance (92.78%; 59.19% vs 33.59% in two cells), lysosomal digestion (6.93%), and exocytosis (0.29%). In summary, this study provided detailed insight of NPs’ fate in cell cycles which is essential for rational design of NPs in the future. Schematic illustration of long-term fate tracking and quantitative analyzing of Prussian blue nanoparticles (PBNPs) - labeled stem cells. Cells are first labeled with PBNPs, then dynamic changes (60 h) of PBNPs-labeled cells are recorded by using live cell imaging system. Combining the proposed pixel-based colorimetry (PBC) quantification method and the investigation of PBNPs lysosomal digestion and exocytosis, the percentage of each factor that contribute to the reduction of intracellular PBNPs content within one cell cycle are summarized. • Long-term tracking of Prussian blue nanoparticles (PBNPs) fate in stem cells at single cell level. • Pixel-based colorimetry method revealed dynamic changes of intracellular PBNPs content during cell interphase and mitosis. • Asymmetric cell inheritance (92.78%) is the main factor contributing the intracellular PBNPs reduction in one cell cycle.