Under the condition of sodium citrate as stabilizer, the gold-selenium (AuSe) nano-alloy was prepared by sodium borohydride reduction procedure, and was modified by single-strand aptamer to obtain an aptamer nano-alloy probe (apta-AuSe) for Hg(Ⅱ). In pH 6.8 Na2HPO4-NaH2PO4 buffer solution and in the presence of NaCl of 33 mmol·L-1, the Apta-AuSe probe is not aggregation. The apta-AuSe interacts with Hg2+ to form stable double-strand T-Hg(Ⅱ)-T mismatches and to release AuSe nano-alloy particles from the probe. The released AuSe nano-alloy particles (20∶1) aggregated to form bigger clusters that resulted in the resonance scattering (RS) intensity (I590 nm) increasing at 590 nm. The increased intensity ΔI590 nm was proportional to the Hg2+ concentration from 1.3 to 1 466 nmol·L-1, with a detection limit of 0.74 nmol·L-1．The regress equation was ΔI590 nm=0.603ｃ+2.0. Thus, a new resonance scattering (RS) spectroscopy of apta-AuSe was applied to the analysis of trace mercury ion. This simple, rapid, selective and sensitive aptamer AuSe nano-alloy RS assay was applied to the determination of Hg2+ in wastewater, with satisfactory results.