Vaporized hydrogen peroxide (VHP) sterilization has been widely used in the fields of medical care and pharmaceuticals. Extracellular polymeric substances (EPS) connected tightly to the cell membrane is first barrier that must be broken through, and less is known about direct change of cell membrane peroxides, and the linkage mechanism among EPS, cell membrane and intracellular damages is still unclear during high concentration VHP sterilization. After optimizing the VHP sterilization process of specific drug-packaging equipment based on the sterility assurance level of 10−6 cfu, we studied the degradation kinetics of exopolysaccharide, exoprotein, extracellular DNA, and investigated the changes of cell membrane lipid/protein peroxides and intracellular peroxidases, and discussed the linkage mechanism of microbial EPS, cell membrane and intracellular damages during high concentration VHP sterilization. The results indicated: (1) The order of degradation kinetics of microbial EPS was exopolysaccharide > exoprotein > extracellular DNA, it was the key to achieve fast and effective VHP sterilization that sufficient high concentration VHP (>400 ppm) was adopted to rapidly destroy EPS (>20 min), resulting in the serious destruction of proteins and lipids of cell membrane; (2) The key mechanism of short time sterilization using high concentration VHP was that the serious loss of the structure/function of cell membrane was the most fatal but the damage of intracellular enzymes and DNA was limited for bacterial cell living.