As low oxygen and high ultraviolet (UV) exposure might significantly affect the microbial existence in plateau, it could lead to a specialized microbial community. To determine the abundance and distribution of ammonia-oxidizing archaea (AOA) in agricultural soil of plateau, seven soil samples were collected respectively from farmlands in Tibet and Yunnan cultivating the wheat, highland-barley, and colza, which are located at altitudes of 3200–3800 m above sea level. Quantitative PCR (q-PCR) and clone library targeting on amoA gene were used to quantify the abundances of AOA and ammonia-oxidizing bacteria (AOB), and characterize the community structures of AOA in the samples. The number of AOA cells (9.34 × 10⁷–2.32 × 10⁸ g^-1 soil) was 3.86–21.84 times greater than that of AOB cells (6.91 × 10⁶–1.24 × 10⁸ g^-1 soil) in most of the samples, except a soil sample cultivating highland-barley with an AOA/AOB ratio of 0.90. Based Kendall’s correlation coefficient, no remarkable correlation between AOA abundance and the environmental factor was observed. Additionally, the diversities of AOA community were affected by total nitrogen and organic matter concentration in soils, suggesting that AOA was probably sensitive to several environmental factors, and could adjust its community structure to adapt to the environmental variation while maintaining its abundance.