As the dominant cyanobacterial species in biological soil crusts (BSCs), Microcoleus vaginatus often suffer from many stress conditions, such as desiccation and high temperature. In this study, the activities of light-harvesting complexes (LHCs) and reaction centers of photosystem II (PS II) in crust cyanobacteria M. vaginatus were monitored under high temperature and desiccation conditions using chlorophyll fluorescence technology. The results showed that all the fluorescence signals were significantly inhibited by high temperature or desiccation treatments. Under high temperature conditions, it was further demonstrated that PS II reaction centers were first destructed within the first hour, then the LHCs gradually dissociated and free phycocyanin formed within 1–5 h, and the activities of all the light harvesting and reaction center pigment proteins were fully suppressed after 24 h of high temperature treatment. Furthermore, the high temperature treated M. vaginatus lost its ability to recover photosynthetic activity. On the contrary, although desiccation also led to the loss of photosynthetic activity in M. vaginatus, after rehydration in the light the fluorescence parameters including Fo, Fv and Fv/Fm could be well recovered within 12 h. It was concluded that desiccation could provide crust cyanobacteria M. vaginatus some protection from other stresses, such as high temperature demonstrated in this experiment. The combine of temperature change and precipitation pattern in the field provide a guarantee for the alternate metabolism and inactivity in crust cyanobacteria. That may be a very important strategy for the survival of crust cyanobacteria in high temperature regions.