The invention relates to an antibacterial thin-layer composite film and a preparation method thereof. The preparation method comprises: carrying out infiltration treatment on the surface of the function layer of a thin-layer composite film by using a carboxylated chitosan coating solution, drying to obtain a carboxylated chitosan film positioned on the surface of the function layer, carrying out infiltration treatment on the carboxylated chitosan film by using a salt solution corresponding to the metal ions in antibacterial nanoparticles and a cross-linking agent solution, and carrying out heat treatment to prepare the antibacterial thin-layer composite film with the cross-linking structure. According to the present invention, the preparation method is simple, the production cost is low, and the prepared antibacterial thin-layer composite film has advantages of high water flux, good antibacterial property and strong antibacterial persistence, and has good industrialized production baseand broad application prospect.