Mercury ion (Hg2+ ) pollution exists in water, soil, and food. By interacting with the thiol groups in protein, Hg2+ ions can accumulate in ways that cause serious damage to the central nervous system and threaten human health and natural environment. Undoubtedly, Hg2+ ion detection is a significant issue in environment and health monitoring. A variety of sensor platforms for Hg2+ ion detection based on organic molecules, DNA, oligonucleotides, inorganic materials, etc, have been reported. In this paper, an artificial peptide PHg, with a cluster bio-mineralize sequence (CCY) and a multi-charge hydrophilic sequence is designed as a template for the one-step synthesis of a peptide-Au cluster probe. Briefly: the peptide PHg in situ anchors Au ions to form a peptide-Au (I) intermediate and the reaction pH with NaOH is adjusted; after 12 h incubation at room temperature, the peptide PHg-Au nanocluster probe with red fluorescence is obtained. The probe has a super-small core size of approximately 1.26 nm and a maximum emission peak at 650 nm. The presence of Hg2+ ions cause the fluorescence of the probe to greatly decrease. Based on the differences in fluorescence intensity of the PHg-Au nanocluster in the absence and presence of Hg2+ ions, Hg2+ ions could be quantitatively detected in concentrations ranging from 5 nmol/L to 1 µmol/L. The limit of detection (LOD) is 7.5 nmol/L. Compared with some interference ions such as, K+, Mg2+, Ca2+, Pb2+, Ni2+, Fe3+, and Cu2+, the selectivity was excellent. The sensing of Hg2+ ion is not affected by the chelate agents: EDTA, which imparts a significant advantage in a range of applications. As a result, a simple, sensitive and selective fluorescent assay based on peptide PHg-Au cluster is developed for the detection of Hg2+ ions.