A novel dual-emission carbon dots-gold nanoclusters (CDs-AuNCs) nanohybrid was fabricated and successfully used in the visual and ratiometric fluorescent detection of mercury (II) ions. Boronic acid functionalized carbon dots (B-CDs) were synthesized by a one-pot hydrothermal method. Bovine serum albumin functionalized carbon dots (BSA-CDs) were then obtained by simply mixing the B-CDs with bovine serum albumin, aided by specific binding between the glycoprotein and boronic acid groups. Finally, the dual-emission nanohybrid was obtained by attaching AuNCs to the BSA-CDs template. The nanohybrid exhibited two well-resolved emission peaks at 440 nm and 655 nm under 360 nm excitation. The fluorescence of the BSA-CDs at 440 nm was insensitive to the presence of aqueous Hg2+, whereas the fluorescence of AuNCs at 655 nm could be completely quenched in the presence of Hg2+ through Hg2+-Au+ interactions. The fluorescence emission of the nanohybrid allowed sensitive and selective sensing of Hg2+ in the range of 2–15 nM, with a detection limit of 0.73 nM. Importantly, the emission color of the nanohybrid changed from red to blue with increasing Hg2+ concentration (due to corresponding changes in the I440nm and I655nm ratio), which could be clearly discerned by the naked eye.