The structure of chitosan membranes chemically modified with aldehydes, such as glutaraldehyde and n-butyl aldehyde, was analyzed. Characteristics of permeation and separation of aqueous ethanol solutions through the membranes were investigated by evapomeation. Chitosan membranes reacted with glutaraldehyde were cross-linked by Schiff base bonds and had no pendant structure. Density and crystallinity of the cross-linked chitosan membranes decreased with increasing glutaraldehyde content in the membranes. The permeation rate, separation factor for water permselectivity, and degree of swelling of the cross-linked chitosan membrane for aqueous ethanol solutions increased with increasing glutaraldehyde content in the chitosan membrane. The structure of the chemically modified chitosan membrane and the permeation and separation characteristics for aqueous ethanol solutions are discussed from the viewpoint of hydrogen bonds of the cross-linked membrane.