Three chitosan derivatives, including carboxymethyl chitosan, N,N,N-trimethyl chitosan and N-metoxybenzenemethyl quaternary ammonium salt of chitosan, were intercalated into the layer of α-ZrP to prepare the nanocomposite materials by the method of microwave irradiation. The structures and morphologies of nanocomposites were characterized by FTIR, XRD, SEM, TEM, TG and zeta potential analysis. The XRD patterns showed that the interlayer spacing of nanocomposites was larger than the original α-ZrP, and the basal spacing of nanocomposites was enlarged with the increasing positive charge of chitosan derivative. It indicated that the chitosan derivative was intercalated into the layer of α-ZrP via hydrogen bonding. The TG experiments showed that the thermal stability of the nanocomposites was improved significantly and much better than that of chitosan. The antibacterial results showed that the nanocomposites had a good antibacterial effect on Escherichia coli and Staphylococcus aureus.