Palygorskite is widely used as industrial adsorbent and also potential for flue gas desulfurization by adsorption of SO2. The effect of thermal treatment on Palygorskite’s structural properties and its performance in SO2 adsorption were investigated. The textural and structural properties of the prepared palygorskite adsorbent were characterized by X-ray diffraction, transmission electron microscopy and temperature programmed desorption. The result showed the channel of Palygorskite is partial collapsed and the structure is not changed ultimately when thermally treated below 300 °C. The structure of Palygorskite is Gradually changed when the treating temperature is higher than 300 °C and is damaged entirety till 800 °C. As a result, the adsorption capacity of SO2 on Palygorskite decreased drastically. It is suggested that the presences of surface adorbed water and zeolitic water which occupy a large number of adsorption sites are disadvantage for the adsorption of SO2, and dissimilarly the presence of crystal-bonded water is favorable.