Lipopolysaccharide (LPS) is a bacterial toxin that causes fever in humans. Our small-molecule chemosensor named Zn-dpa-C2OPy shows rapid ratiometric fluorescence response to LPS in water with a detection limit of 11 pM, which is lower than that of our previously reported sensor. Spectroscopic measurements (fluorescence, absorbance, 1H NMR, and fluorescence lifetime), dynamic light scattering measurements, and transmission electron microscopy observations revealed that the fluorescence response was induced by the changes in the aggregation state via multi-point recognition of LPS through hydrophobic and electrostatic interactions, in addition to the coordination between the zinc(II)-dipicolylamine moiety of the chemosensor and the phosphate group of LPS. The proposed Zn-dpa-C2OPy chemosensor was applied to an original flow injection analysis (FIA) system with a self-developed dual-wavelength fluorophotometer, and a high throughput of 36 samples per hour was achieved. These results demonstrate the feasibility of this unique methodology combining a ratiometric fluorescent chemosensor and FIA for continuous online monitoring of LPS in water.