Graphitic carbon nitride quantum dots (CNQDs) are a new class of nanomaterial with an extraordinary photoluminescent property. Here, three highly water-soluble and photo-luminescent CNQDs are synthesized through a green and facile one-step hydrothermal approach, with urea as the nitrogen source and citric acid and its salts as carbon sources. The photoluminescence (PL) performance demonstrated that the fluorescence emission peak was altered by neither the structures nor the molar ratio of urea to the carbon source. Three highly luminescent CNQDs with a quantum yield of 40% were obtained when the molar ratio of urea to sodium citrate, citric acid, and ammonium citrate was 6:1, 18:1, and 18:1, which have average sizes of 4.1, 4.6, and 6.3 nm, respectively. Moreover, the possibility of using CNQDs as potential probes to determine the concentration of iron is also discussed. The results show that the as-prepared CNQDs has high selectivity for Fe3+ ions. The quenching mechanism of CNQDs by iron is connected with the nitrogen functional groups on the surface of CNQDs. Results showed valuable information about the effects of the carbon source on the PL efficiency, biocompatibility, and metal ion detection properties of CNQDs.