Soil is the place where plants colonize and an important interface between plant and microorganism interaction. Archaea is an important component of soil microorganism and plays an important role in the biogeochemical cycle of carbon, nitrogen, sulfur and iron, and in the growth, the development and adaptation to the environment of plants. It is rarely reported the influence of plant colonization on the archaeal community in soil. The relict plants have special advantages in the study of interaction among plant, microbe and environment. In this paper, the archaea in rhizosphere soil in relict plant Tetraena mongolica and barren soil obtained from three different communities of desert plants including the community of Tetraena mongolica, Reaumuria songarica, Salsola passerine and Stipa capillata, the community of Tetraena mongolica and Stipa capillata and the community of Tetraena mongolica where Tetraena mongolica is the dominant species or constructive species were studied to explore the effect of relict plant Tetraena mongolica colonization on the number, the diversity, the composition and the function of archaeal community using the high-throughput sequencing method. The results showed that the diversity and the number of species in archaeal community of rhizosphere soil increased with relict plant Tetraena mongolica colonization. Meanwhile, the composition of archaeal community in soil were changed with relict plant Tetraena mongolica colonization. The relative abundance of ammonia oxidizing archaea of genera unclassified_f_Nitrososphaeraceae of phylum Thaumarchaeota and ammonia oxidizing archaea of Candidatus Nitrososphaera of phylum Thaumarchaeota in rhizosphere soil decreased, while the relative abundance of ammonia oxidizing archaea of genera Candidatus Nitrocosmicu of phylum Thaumarchaeota and norank_o_Marine_Group_II of phylum Euryarchaeota in rhizosphere soil increased. There was no obvious change on the relative abundance of unclassified_c__Thermoplasmata of phylum Euryarchaeota. However, the succession of plant communities had no significant effect on the archaea communities in the rhizosphere soil of relict plant Tetraena mongolica and barren soil. Ammonia oxidizing archaea of family Nitrososphaeraceae is the core microbiome of archaeal communities in soil obtained from three different communities of desert plants. Furthermore, the relict plant Tetraena mongolica colonization greatly changed the function of archaeal community in soil. The high abundant function of archaeal community in soil was weakened and the low abundant function of was enhanced. There was significant effect on aerobic respiration, the pathway of nucleotide biosynthesis and the pathway of amino acid biosynthesis.The relict plant Tetraena mongolica colonization has changed characteristics of archaeal community in desert soil including the number of species, the diversity and the species composition, the function, etc.