This paper presents a novel method for directly imaging and counting bacteria at single cell level under low optical resolution condition by inducing nanoprobes aggregation on the cell surface and forming cell-core shell particles. Two kinds of gold nanoprobes with polyethyleneimine (PEI-AuNPs) and citrate (SC-AuNPs) modified respectively have been fabricated and could form quick multi-layer adsorption on the bacteria cells. The adsorption leads to a visible precipitate particle which could be automatically imaged and counted in the microdroplet. To validate the method, E.coli samples has been quantified in less than 0.5 hour. Compared with traditional plate-spread counting and PCR, no time-consuming procedures of culture and high cost biochemical reagent needed in the developed method.