Microcoleus vaginatus, the dominant species in the algal crust in desert regions, plays a significant role in the early development stage of the algal crust. In this study, we examined each development stage of the crusts under laboratory setup to explore the effect of different compositions of M. vaginatus on the algal biomass and crust thickness and hardness. In addition, we studied the physical interactions based on the observation of microstructure of the algal crust with the assistance of light microscopy and scanning electron microscopy, this paper analyzes the cementation style and mechanism of sand grains in different stages. We found that: (1) In the early stage of the crust development the crust was thin and fragile with a hardness of merely (12.21±1.58) Pa. At this stage the crust was formed by aggregating sand particles through adhesive materials which were made of extra\|cellular polymeric substances, excreted by microorganisms or algae. With further development of the algal community the M. vaginatus became the dominant species and the crust was maintained mainly through the mechanical binding of filaments surrounding sand particles at this stage. As a result, the crust became thicker and stronger with a organic layer on the surface. (2) The algal biomass and the crust thickness and hardness increased with the increase of the proportion of M. vaginatus (P < 0.01), with the maximum biomass and the highest crust thickness and hardness occurred at 80% of M. vaginatus in the total algal biomass. However, with further increase in the M. vaginatus proportion the algal biomass and the highest crust thickness and hardness started declining. This study provided valuable data and experimental methods for further investigating the dynamics and functions of the desert algal crust ecosystems and for desert ecosystem restoration.