In this paper, algal crusts collected from desert soil of the east side of the Helan Mountain were used as samples to study the microbial communities and their succession during early development of biological soil crusts. 521 16S rDNA OTUs and 64 18S rDNA OTUs were obtained from all samples via high throughput sequencing, which showed that diversity of prokaryotes was obviously higher than that of eukaryotic microorganisms. Prokaryotes in algal crusts were distributed in 26 classes. Cyanobacteria was the dominant microbial group in 4 development stages samples. Actinobacteria, Chloroplast, Alphaproteobacteria, and Bacilli were also higher relative abundance in all stages of samples. In the taxonomic level of genera, Bacillus, Leptolyngbya, Microcoleus, Microvirga, Chroococcidiopsis, Rubellimicrobium, Phormidium, Mastigocladopsis, Skermanella, Nostoc, and Scytonema existed in all stages of samples, but the abundance of each of them were different. The relative abundance of Bacillus was higher in the formation stage, initial stage, and intermediate stage samples, but decreased significantly in maturity stage samples. On the contrary, the relative abundance of Microvirga increased significantly in maturity stage samples. The above results indicated that there was obvious succession of bacterial communities. Eukaryotic microorganisms in samples were distributed in 13 classes. The abundance of Dothideomycetes and Pezizomycetes were higher in all stages samples. The abundance of Agaricomycetes was as high as 32.6% in formation stage, however, its abundance was declined rapidly in the development process of algal crusts. The abundance of protists increased gradually with development of algal crusts. No sequence of eukaryotic microalgae was found in all stages of samples. Thirteen genera of eukaryotic microorganisms which had taxonomic information were found in samples. In which, Coniothyrium, Dendryphion, Friedmanniomyces, Phloeopeccania, and Sarocladium occurred in all stages samples, and the rests occurred only in individual stage samples. The results showed that the eukaryotic microorganisms community also had been changing with the development of algal crusts. The main factors on microbial community were thickness, total nitrogen and organic maters of crusts.