The present work reports a sensitive and selective fluorescent sensor for the detection of mercury ion, Hg(II), by hybridizing carbon nanodots (C-dots) and gold nanoclusters (Au NCs) through intrinsic interactions of the two components. The C-dots serve as the reference signal and the Au NCs as the reporter. This method employs the specific high affinity metallophilic Hg²⁺–Au⁺ interactions which can greatly quench the red fluorescence of Au NCs, while the blue fluorescence of C-dots is stable against Hg(II), leading to distinct ratiometric fluorescence changes when exposed to Hg(II). A limit of detection of 28 nM for Hg(II) in aqueous solution was estimated. Thus we applied the sensor for the detection of Hg(II) in real water samples including tap water, lake water and mineral water samples with good results. We further demonstrated that a visual chemical sensor could be manufactured by immobilizing the nanohybrid probe on a cellulose acetate circular filter paper. The paper-based sensor immediately showed a distinct fluorescence color evolution from pink to blue after exposure to a drop of the Hg(II) solution.