Soil biological crusts distribute widely in arid environment, and high temperature stress is a critical environmental factor on algal survival in these areas. During summer and autumn, temperature of desert biological crusts rise rapidly under the intense sun radiation. Scytonema javanicum Born et Flah is one of the important dominant species in biological soil crust and distributes at the outermost layer of biological soil crust. Consequently, S. javanicum are often suffered from high temperature. It is necessary to take into account the survival of S. javanicum in the desert environment. However, the impact of high temperature on desert algae was rarely reported. So, S. javanicum was used as experimental material, the effect of different high temperature (25℃ as control, 35℃, 40℃ and 45℃) on physiological, biochemical characteristics, and cell structure were studied in the laboratory in order to illuminate the tolerance and adaptation mechanisms of desert algae under high temperature. The results showed that chlorophyll a synthesis increased while carotenoid synthesis decreased under 35℃; on the contrary, carotenoid synthesis accelerated while chlorophyll a synthesis retarded under 40℃, contents of carotenoid in 40℃ were significant higher than those in control and 35℃ treaments. Changes of photosynthetic pigment content in S. javanicum under different temperatures generated variance in photosynthesis efficiency. As for the short term (6h) treatments, the maximum photochemical efficiency (Fv/Fm) and actual photochemical efficiency (PSII) of S. javanicum were significantly promoted under 35℃, while Fv/Fm and PSII were inhibited under 40℃. For 45℃ treatments, photosynthetic activity of S. javanicum could not be detected after 2h, whose photosynthetic organs were irreversibly damaged and could not be restored. As to the long term (15d) treatments, there was no significant difference between 35℃ treatments and controls in Fv/Fm and PSII of S. javanicum. However, the maximum photochemical efficiency (Fv/Fm) and actual photochemical efficiency (PSII) of S. javanicum were noticeably restrained in 40℃ treatments. With the increasing of temperature, lipid peroxidation in S. javanicum increased gradually, and content of malondialdehyde (MDA) also enhanced. MDA contents of S. javanicum in 40℃ treatments were significant higher than those in control and 35℃ treatments. At the same time, with the temperature increasing, the membrane structures in cells of S. javanicum were more and more fragile. And the polysaccharides, as osmotic regulation substances, play important roles in preventing the damages of high temperature on membrane. Accordingly, the higher the temperature was, the more the contents of extracellular polysaccharides and intracellular soluble sugar outside and inside S. javanicum. Especially, content of extracellular polysaccharides outside S. javanicum in 40℃ treatments was almost 8 times than that of controls. Photographs of transmission electron microscope (TEM) sections of S. javanicum showed that cell structures were not damaged in 35℃ treatments, cellular morphologies were more stable, while the ultrastructures of algal cells were significantly damaged in 40℃, the protoplasts were flocculent and vacuolar finally. All these results confirmed that S. javanicum could withstand appropriate high temperature (35℃). This study has some theoretical significance in understanding the tolerance and adaptability of S. javanicum to high temperatures, and has actual guidance value in controlling desertification by use of desert cyanobacteria.