Jellyfish Cyanea nozakii venom is a complex mixture of various toxins, most of which are proteinous biological macromolecules and are considered to be responsible for clinical symptoms or even death after a severe sting. Previous transcriptome and proteome analysis identified hundreds of toxins in the venom, including hemolysins, C-type lectin, phospholipase A2, potassium channel inhibitor, metalloprotease, etc. However, it is not clear which toxin in the venom plays the most important role in lethality. Herein, we isolated the key lethal toxin (Letoxcn) from jellyfish Cyanea nozakii using anion exchange chromatography, size-exclusion chromatography, and cation exchange chromatography. The molecular weight of Letoxcn is ∼50 kDa with the N-terminal sequences of QADAEKVNLPVGVCV. Peptide mass fingerprinting analysis of Letoxcn shows that it may have some motifs of phospholipase, metalloproteinase, thrombin-like enzyme, potassium channel toxin, etc. However, only metalloproteinase activity but no hemolytic, PLA2, or blood coagulation activity was observed from in vitro toxicity analysis. Overall, this study uncovered and characterized the key lethal toxin in the venom of jellyfish Cyanea nozakii, which will not only help to reveal the molecule mechanism of the lethality, but also develop effective treatment like antivenom for this jellyfish sting in the future.