The antibacterial PET (polyethylene terephthalate) masterbatch was extruded from twin screw extruder, using silver and zinc-loading Nano-SiO2 antibacterial agent (SLSZ) as the functional material. The content of SLSZ and extruding techniques were investigated. The dispersion and compatibility of antibacterial agent in antibacterial PET masterbatch were further characterized using Scanning Electron Microscopy and Transmission Electron Microscopy. The antibacterial performances and adsorption process of the antibacterial PET masterbatch against Escherichia coli (E. coli) were tested using alive-bacteria-counting method. The experimental results indicate that when the content of SLSZ was 30 wt. %, the antibacterial agent with an average diameter of 150nm showed excellent dispersion and compatibility in antibacterial PET masterbatch, and had excellent antibacterial performances. The adsorption process of antibacterial PET masterbatch against E. coli was controlled by Coulomb force between them. As the amount of the antibacterial PET masterbatch increased, the adsorbing rate and capacity were increased.