Chitosan (CS) nanocomposite mesoporous membranes were fabricated by mixing CS with graphene (G) and fullerene (F) nanofillers, and the diffusion properties through CS membranes were studied. In addition, in order to enhance the binding between the internal CS chains, physical cross‐linking of CS by sodium tripolyphosphate (TPP) was carried out. F and G with different weight percentages (0.1, 0.5, and 1 wt.%) were added on physically cross‐linked chitosan (CLCS) and non‐cross‐linked chitosan (NCLCS) membranes by wet mixing. Permeability and diffusion time of CLCS and NCLCS membranes at different temperatures were investigated. The results revealed that the pore size of all fabricated CS membranes is in the mesoporous range (i.e., 2–50 nm). Moreover, the addition of G and F nanofillers to CLCS and NCLCS solutions aided in controlling the CS membranes’ pore size and was found to enhance the barrier effect of the CS membranes either by blocking the internal pores or decreasing the pore size. These results illustrate the significant possibility of controlling the pore size of CS membranes by cross‐linking and more importantly the careful selection of nanofillers and their percentage within the CS membranes. Controlling the pore size of CS membranes is a fundamental factor in packaging applications and membrane technology.