Stem cells reside in a three-dimensional (3D) niche microenvironment， which provides specific cues， including cell-matrix interactions and soluble factors， that are essential to the differentiation of stem cells in vivo. Herein we demonstrate a general approach to the synthetic reconstruction of 3D biomimetic niche environment of stem cells by the multiscale combination of macroscopic porous hydrogels and a nanoscale upconversion nanoparticles (UCNP)-based nanocomplex. The porous biopolymeric hydrogels emulate the spongy bone microstructure and provide 3D environment conducive to the differentiation of seeded stem cells. The UCNP-based nanocomplex (Pur-UCNP-peptide-FITC)， which is stably encapsulated in the porous hydrogels， emulates the repertoire of inductive factors in bone matrix by maintaining localized long-term delivery of inductive small molecules. The nanocomplex also generates biomarker-specific reporting emissions that correlate with the extent and stage of differentiation of the stem cells in synthetic niche， thereby allowing long-term tracking of stem cell fate in a non-contact， non-destructive， and potentially high-throughput manner in living cultures. To the best of our knowledge， this is first demonstration of synthetic niche reconstruction. The modular nature of this synthetic niche platform allows various parameters to be easily tuned to accommodate a variety of fundamental studies of dynamic cellular events under controlled settings.