The absolute abundance of amoA genes of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and complete ammonia oxidizer (CMX) in three typital habitats of Qinghai-Tiket Plateau were determined by the qPCR, and the community structures of AOA, AOB and nitrite-oxidizing bacteria (NOB) were analyzed by using the Illumina HiSeq sequencing of the 16S rRNA gene amplicons. The qPCR demonstrates that the abundance of amoA genes of ammonia oxidizers is in the order AOA>CMX>AOB in the desert grassland and alkaline saline soils, but CMX≥AOA>AOB in the wetlands. The 16S rRNA gene amplicon analysis reveals that the AOA mostly are belonged to the Nitrosocosmicus clade of the soil group 1.1b in nearly all three habitats, which is also detected in the Arctic soils. Nitrosospira is the predominant genus in the desert grassland and wetland with 71.21%-100% of all AOB sequences, but 75.51%-88.71% of AOB in alkaline saline soils fall into the genus of Nitrosomonas. However, NOB of all three habitats are mostly affiliated with the genus of Nitrospira with 70.87%-98.79% of all NOB sequences. Both clade A and B of CMX are detected in all three habitats and with the similar relative abundances. Notably, most habitats in this study harbor typical lineages of nitrifier specific from marine ecosystems, for instance, group 1.1a of AOA, N. marina of AOB and lineage 4 of NOB, strongly indicating that these nitrifying communities are also influenced by the paleo-ocean environment since the Qinghai-Tibet Plateau was Tethys Sea 500 Ma year ago.