Carbon dots (CDs) emitting red fluorescence (610 nm) were synthesized by solvent thermal treatment of p-phenylenediamine in toluene. Upon 440 nm excitation, quercetin (QCT) alone endowed slight effects on the red fluorescence of CDs. Once Zn2+ was further introduced, the QCT-Zn2+ complex was quickly formed. This complex absorbs excitation light and emits bright green fluorescence at 480 nm. The red fluorescence of CDs was greatly quenched owing to the inner-filter effect. The ratio of fluorescence intensity at 480 nm and 610 nm (I480/I610) gradually increases with increasing concentration (c) of Zn2+. Al3+ exhibits the same phenomen like Zn2+. Fluoride ions form a more stable complex with Al3+ than QCT-Al3+ complex but have a negligible effect on the QCT-Zn2+ complex. The possible interference of Al3+ on Zn2+ can thus be avoided by adding certain amount of F−. The CD-QCT-F− system was constructed as a ratio-metric fluorescent nanoprobe toward Zn2+ with determination range of 0.14–30 μM and limit of detection (LOD) of 0.14 μM. Due to the stronger affinity of adenosine triphosphate (ATP) to Zn2+ than QCT, the I480/I610 value of CD-QCT-F−-Zn2+ system gradually decreases with increasing cATP. The ratiometric fluorescent nanoprobe toward ATP was established with detection ranges of 0.55–10 and 10–35 μM and a LOD of 0.55 μM. The above two probes enable the quantitative determination of Zn2+ and ATP in tap and lake water samples with satisfactory recoveries. Graphical abstractSchematic representation of the ratiometric fluorescent nanoprobes based on the carbon dots (CDs)-quercetin (QCT) system towards Zn2+ and adenosine triphosphate (ATP) with high selectivity and sensitivity.