In order to develop a new type of disinfection material for water treatment, a new kind of antibacterial material named quaternized chitosan/ silver nanoparticles (QCS/nAg) was prepared by using quaternized chitosan as a modifier of silver nanoparticles, which has synergetic effect and positively charged surface. To study the antibacterial performance of QCS/nAg, neutrally charged and negatively charged nanoparticles were used as comparison to inactivate bacteria, especially Escherichia coli, in water. The function of QCS and nAg in composite materials was evaluated. Furthermore, the antibacterial influencing factors such as material dosage, pH value, and chloride ions were studied. The antibacterial mechanism of QCS/nAg was concluded through studying the dissolution of QCS/nAg and the reaction between QCS/nAg and bacteria, including adsorption and damage of cell wall (cytomembrane). Results showed that QCS/nAg with high dispersibility was successfully synthesized and it performed better inactivation effect than other nAg. QCS and nAg showed synergetic effect in QCS/nAg when treated with bacteria. Compared with PVP/nAg, QCS/nAg exerted superiority in dosing quantity and resistance to interference of chloride ion. The antibacterial mechanism was summarized as that QCS/nAg strengthened the adsorption process of bacteria and the damage to the cell wall (cytomembrane).