The invention discloses a quaternized chitosan / polyacrylic acid composite nanofiltration membrane and a preparation method thereof. The preparation method comprises the following steps: by a layer-by-layer deposition method, taking positively-charged 2-hydroxypropyl trimethylammonium chloride chitosan as a cationic polymer and polyacrylic acid as an anionic polymer, then introducing a NaCl solution as a supporting salt, alternately depositing, self-assembling layer by layer to form a composite membrane, and finally crosslinking in epoxy chloropropane to obtain the composite nanofiltration membrane. The preparation method provided by the invention is simple in process, natural and environment-friendly; the prepared positively-charged composite nanofiltration membrane has good hydrophilicity, excellent mechanical properties and an excellent swelling property, has the purified water permeation coefficient of 19.29L.h<-1>.m<-2>.Mpa and the cutoff molecular weight of 989, and can be used for separating and removing micro-trace pollutants, especially the positively-charged substances, in a water environment.