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A multiple turn-on fluorophore (FHCS), combining fluorescein, hydrazone, cyanuric chloride and salicylaldehyde chromone into a molecule, was identified and developed based on density functional theoretical calculation. It was expected that FHCS could express exclusive fluorescent signals and improved Stokes shifts when chelating Al3+ or Zn2+. After it was synthesized and characterized in detail, it was noted that FHCS could turn-on fluorescently discriminate trace Al3+ and Zn2+ under the optimized conditions, i.e., from no-fluorescence to strong blue fluorescence for Al3+ and to green fluorescence for Zn2+ with low detection limits of 5.37 × 10−8 M and 7.90 × 10−8 M respectively. Owing to its low toxicity, FHCS was successfully applied for quantitative determination of Al3+ and Zn2+ in natural aqueous samples and toxicity evaluation of Al3+ and Zn2+ in living cells and bio-tissues with excellent linear relationships. The action mechanisms for FHCS with Al3+ and Zn2+ were confirmed to form stable 5-member-co-6-member condensed rings between Al3+/Zn2+ and N/O atoms in FHCS by both theoretic and experimental methods, which resulted in turn-on fluorescence with different dipolar moments and improved Stokes shifts. A multiple turn-on fluorophore, combining fluorescein, hydrazone, cyanuric chloride and salicylaldehyde chromone into a molecule (FHCS), was identified and developed for turn-on fluorescently discriminate trace Al3+ and Zn2+ in natural aqueous, living cells and bio-tissue samples with quite low detection limits of 5.37 × 10−8 M and 7.90 × 10−8 M respectively. The action mechanisms for FHCS with Al3+ and Zn2+ were confirmed by both theoretic and experimental methods to form stable 5-member-co-6-member condensed rings between Al3+/Zn2+ and N/O atoms, which resulted in turn-on fluorescence with different dipolar moments and improved Stokes shift. Image 1 • A multiple turn-on fluorophore combining fluorescein, hydrazone, cyanuric chloride and salicylaldehyde chromone was developed. • It could turn-on fluorescently monitor Al3+ and Zn2+ in aqueous. • It was applied for cell imaging of Al3+ and Zn2+ in bio-samples. • The reaction mechanism was to form stable 5-member-co-6-member condensed rings with improved Stokes shift. [ABSTRACT FROM AUTHOR]