Recently, many studies on the 3-dimensional (3D) fabrication of cells have been performed. Under these circumstances, it is indispensable to develop the imaging technologies and methodologies for non-invasive visualization of 3D cells fabricated. The objective of this study is to develop the labeling method of human induced pluripotent stem (iPS) cells-derived 3D cartilage tissue with gelatin nanospheres co-incorporating 3 kinds of quantum dots (QD) and iron oxide nanoparticles (IONP) (GNSQD+IONP). In this study, two labeling methods were performed. One is that a cartilage tissue was labeled directly by incubating with octa-arginine (R8)-treated GNSQD+IONP (direct labeling method). The other one is a "dissociation and labeling method". First, the cartilage tissue was dissociated to cells in a single dispersed state. Then, the cells were incubated with R8-GNSQD+IONP in a monolayer culture. Finally, the cells labeled were fabricated to 3D pellets or cell sheets. By the direct labeling method, only cells residing in the surrounding site of cartilage tissue were labeled. On the other hand, the 3D cartilage pellets and the cell sheets were homogenously labeled, and maintained fluorescently visualized over 4 weeks. In addition, the cartilage properties were histologically detected even after the process of dissociation and labeling. Homogenous labeling and visualization of human iPS cells-derived 3D cartilage tissue was achieved by the dissociation and labeling method with GNSQD+IONP.