Electrochemistry has been widely used to explore fundamental properties of single molecules due to its fast response and high specificity. However, the lack of efficient signal amplification strategies and quantitative method limit its clinical application. Here, we proposed a digital single virus electrochemical enzyme-linked immunoassay (digital ELISA) for H7N9 avian influenza virus (H7N9 AIV) counting by integration of digital analysis, bifunctional fluorescence magnetic nanospheres (bi-FMNs) with monolayer gold nanoparticles (Au NPs) modified microelectrode array (MA). Bi-FMNs are fabricated by coimmobilizing polyclonal antibody (pAb) and alkaline phosphatase (ALP). At most, one target will be captured per bi-FMNs by controlling the proportion of bi-FMNs to target concentrations (≥5:1). The introduction of digital analysis can solve signal fluctuation and the reliability of single virus detection, enabling the digital ELISA to be sensitively and accurately applied for H7N9 AIV detection with a low detection limit of 7.8 fg/mL, which is greatly promising in single biomolecular detection, early diagnosis of disease, and practical application.