The variation analysis of membrane properties including membrane thickness and pore-size was carried out theoretically by using affinity-membrane model based upon the Freundlich adsorption equation. As the percentage variation of membrane thickness and distribution of pore-size increase, we find that (1) the time of total saturation is delayed; (2) the loading capacity at the point of breakthrough are decreased; (3) solute recovery efficiency and ligand utilization efficiency is decreased; (4) the thickness of unused membrane is increased. The results show that even small variations of thickness and distribution of pore size may severely degrade the membrane performance.