Structure of leaf epidermis and chloroplast of common reed (Phragmites communis Trin.) inhabiting in three different habitats in the Tengger Desert of northwest China were investigated, and they are dune reed (DR); Gobi salt reed (GSR) and swamp reed (SR). Leaf epidermis, mesophyll cells and chloroplasts were detected by scanning electron microscopy and transmission electron microscopy, respectively. The results indicate that foliar surface and mesophyll have different adapting responses in reed in these three different habitats. Compared to SR, the two terrestrial ecotypes, DR and GSR, have lower stomatal densities and smaller caliber of stomata. The stomata caved in the leaf surface and a number of crystals like hairs accumulate in the epidermis in DR and GSR, especially in GSR. A particular structure similar to salt gland is found in GSR. In addition to differences in the surface, the two terrestrial ecotypes also exhibit mesophyll differences compared to SR. Chloroplasts in mesophyll cells are attached to the cell wall and exhibit a long shuttle shape in the two terrestrial ecotypes and an ellipsoid shape chloroplast in SR. Higher density of starch grain is exhibited in GSR. These results suggest that the adaptation of common reed to saline or drought-prone dunes triggers changes in the organs related to apperceive environmental conditions could contribute to the high resistance of reeds to extreme habitats.