Phosphonates are efficient corrosion and scale inhibitors commonly used in industrial circulating water systems. However, conventional detection methods cannot accurately detect their concentration in some water bodies and sludge because of their low concentration. In this study, a ratiometric fluorescent probe was constructed based on quercetin (QC) and divalent zinc ion (Zn2+) to comparatively detect three typical phosphonates for the first time. Compared with the naked QC, Zn2+-quercetin complex (ZnQC) in the designed probe shows considerable differences in terms of luminescence properties and surface morphology. When the concentration of QC and Zn2+ were 10 mM and 50 μM, the detection limits for ATMP, HEDP, and DTPMPA were 0.223, 0.205 and 0.152 μM, respectively, which were lower than of the corresponding values obtained through the chromatography method and phosphomolybdenum blue spectrophotometry. Moreover, for the first time, the quantitative analysis of molecular surface, basin analysis, and atoms in molecules (AIM) analysis and non-covalent interaction analysis (NCI) in the Multiwfn program were employed to investigate the binding sites of QC with Zn2+. The electron excitation properties were further analyzed via theoretical calculations based on the dependent density functional theory (DFT) and time-dependent density functional theory (TDDFT). The detection mechanism can be ascribed to the static quenching considering the formation of non-fluorescent ground-state complexes. Additionally, the ratiometric probe demonstrated some features such as high sensitivity, selectivity, and a simpler operation which has been applied to detect practical water samples with satisfactory results.