A new, highly sensitive and selective sensor for the electrochemical assay of Hg(II) by anodic stripping voltammetry has been developed, whereby a glassy carbon electrode is modified with a novel inorganic-organic hybrid nanocomposite, namely, bimetallic Au-Pt nanoparticles/organic nanofibers (labeled as Au-PtNPs/NFs). The sensor possesses a three-dimensional (3D) porous network nanoarchitecture, in which the bimetallic Au-Pt NPs serving as metal NP-based microelectrode ensembles are homogenously distributed in the matrix of interlaced organic NFs. The surface structure and composition of the sensor were characterized by scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy (XPS). Its electrochemical performance was systematically investigated. Our results show that such a newly designed, Au-PtNPs/NF nanohybrid modified electrode provides remarkably improved sensitivity and selectivity for the stripping assay of Hg(II). The detection limit is found to be as low as 0.008 ppb (S/N = 3) that is much below the guideline value from the World Health Organization (WHO). Interferences from other heavy metal ions such as Cu(II), Cr(III), Co(II), Fe(II), Zn(II), and Mn(II) ions associated with mercury analysis are effectively inhibited. Toward the goal for practical applications, the sensor was further evaluated by monitoring Hg(II) in tap and river water specimens.