Graphene quantum dots (GQDs) have been widely used as fluorescence probes to detect metal ions with satisfactory selectivity. However, the diverse chemical structures of GQDs lead to selectivity for multiple metal ions, and this can lead to trouble in the interpretation of selectivity due to the lack of an in depth and systematic analysis. Herein, bare GQDs were synthesized by oxidizing carbon black with nitric acid and used as fluorescent probes to detect metal ions. We found that the specific ability of GQDs to recognize ferric ions relates to the acidity of the medium. Specifically, we demonstrated that the coordination between GQDs and Fe3+ is regulated by the pH of the aqueous GQDs solution. Dissociative Fe3+ can coordinate with the hydroxyl groups on the surface of the GQDs to form aggregates (such as iron hydroxide), which induces fluorescence quenching. A satisfactory selectivity for Fe3+ ions was achieved under relatively acidic conditions; this is because of the extremely small Ksp of ferric hydroxide compared to those of other common metal hydroxides. To directly survey the key parameter for Fe3+ ion specificity, we performed the detection experiment in an environment free of interference from the buffer solution, noninherent groups, and other complex factors. This study will help researchers understand the selectivity mechanisms of GQDs as fluorescence probes for metal ions, which could guide the design of other GQD-based sensor platforms.