Polyelectrolyte complex based on two anionic polysaccharides, composed of sodium alginate and carrageenan, were prepared by interacting with divalent calcium ions in solution. The effects of annealing on the structural deformation of polyelectrolyte complex and on their characteristics at removing water from a methanol mixture from the point of molecular sieve were investigated and discussed. The result showed that the structural deformation of the annealed polyelectrolyte complex has an effect on the free volume between these polymer chains and the chelate segments such a shrinking of the overall morphology, which act as a molecular sieve in the separation of methanol and water mixtures.