Fluorescent metal‐organic frameworks (MOFs) have been evolved as a class of promising materials for sensing application. However, it is still a challenging issue to understand the sensing mechanism of luminescent MOFs interacting with analyte species from molecule level. Herein, fluorescent Sc2(NH2‐BDC)3 crystals are prepared as a probe. The compositional and structural characteristics of the obtained product are systematically characterized. Sc2(NH2‐BDC)3 shows admirable thermal and chemical stability in different solvents and aqueous solutions with diverse pH values. It shows excellent fluorescence sensing behaviors towards Co2+ and Ni2+ ions through fluorescence quenching effect. The sensing mechanism of Sc2(NH2‐BDC)3 towards heavy metal ions is elucidated via X‐ray photoelectron spectroscopy (XPS) analyses, Fourier transform infrared (FTIR) spectroscopy analyses, solid‐state NMR (ssNMR) spectra and electron paramagnetic resonance (EPR) analyses. The as‐prepared Sc2(NH2‐BDC)3 crystals contain some defects with formation of scandium hydroxyls in the crystal structure from the evidence analyzed by ssNMR and EPR, which are inclined to interact with Co2+ and Ni2+ ions, leading to the fluorescent quenching. This research not only demonstrates the understanding of the sensing mechanism of luminescent MOFs from molecular level, but also highlights the design of functionalized MOFs for fluorescent sensing.