Herein, we report a facile, ultrasensitive, and selective fluorescence turn-on sensing strategy based on green-light-emitting functional nanodots for the detection of bacterial lipopolysaccharide (LPS) endotoxin. In this protocol, first, the pure carbon dots (CDs) with a fairly high quantum yield were prepared by microwave-assisted pyrolysis of citric acid in the presence of urea. Subsequently, the carboxyl-group-rich surfaces of the CDs were allowed to conjugate with the poly-l-lysine (PLL) using an EDC-NHS amidization method to obtain the PLL-modified CDs (PLL-CDs). The LPS could specifically bind to the PLL at the PLL-CD surfaces, and this binding enabled an electron transfer from the phosphate groups of LPS to the carbon core through the PLL bridge, thus resulting in a fluorescence enhancement. Interestingly, this fluorescent turn-on sensor provided a detection limit of 68.3 fM in PBS (pH 7.4), which is the lowest ever reported among all of the synthetic assays for LPS detection. Furthermore, our fluorescent probe was able to show a remarkable selectivity toward LPS over a range of commonly known interfering substances. Thus, this study demonstrated the feasibility of using specific LPS binding to PLL to drive molecular recognition in aqueous medium and offered an effective fluorescence turn-on sensing strategy to detect bacterial endotoxin in diverse clinical and biological applications.