N,O-(2-carboxyethyl)chitosan (N,O-2-CEC) was prepared from chitosan with 3-chloropropionic acid as modifying agent and NaOH as catalyst. Different quaternary ammonium groups were introduced into N,O-2-CEC by the reaction between N,O-2-CEC and different 2,3-epoxypropyl trialkyl ammonium chlorides in the presence of 25% NaOH aqueous solution, and obtained different quaternized N,O-2-carboxyethyl chitosans (QCECs). Structures of QCECs were characterized by FT-IR, (HNMR)-H-1 and gel permeation chromatography (GPC). Antimicrobial activity of QCECs was evaluated against a gram-negative bacterium Escherichia coli and a gram-positive bacterium Staphylococcus aureus. Compared with N,O-2-CEC and quaternized chitosans, the QCECs had much stronger antimicrobial activity, which increased with increasing chain length of the alkyl in the quaternary ammonium groups. The presence of benzyl in quaternary ammonium groups could endow QCECs with much better antimicrobial activity.