An ultrasensitive and specific-selection electrochemical sensor was constructed for Hg2+ detection based on Au nanoparticles and molybdenum selenide (Au NPs@MoSe2) as well as the thymine-Hg2+-thymine (T-Hg2+-T) coordination. Herein, Au NPs@MoSe2 not only could improve the sensitivity due to the large surface area and good electrical conductivity but also offered more sites to immobilize thiol-labeled T-rich hairpin DNA probes (P-1), which has a specific recognition for Hg2+ and methylene blue-labeled T-rich DNA probes (MB-P). When Hg2+ and MB-P exist, P-1 and MB-P can form a stable T-Hg2+-T complex. Then, methylene blue can be close to the electrode and detectable via differential pulse voltammetry (DPV). Benefiting from the specific recognition of T-Hg2+-T and the merits of Au NPs and MoSe2, the fabricated biosensor presented an ultrasensitive and highly selective performance. The DPV responses had a positive linear relationship with Hg2+ concentrations over ten orders of magnitude from 1.0 × 10-16 to 1.0 × 10-7 mol L-1. The detection limit was down to 1.1 × 10-17 mol L-1. Moreover, the developed sensor exhibited a promising application for trace Hg2+determination in water samples.