Soil ammonia oxidizers play essential roles in nitrogen cycling in many forest ecosystems. Since the compositions and functions of soil ammonia oxidizer could be suffered from obviously seasonal snow cover and freeze-thaw cycles in high latitude/altitude region, there might be significant differences of soil ammonia oxidizer in different periods caused by seasonal freeze-thaw cycles. However, little attention has been paid to the variations of soil ammonia oxidizer in different key periods in subalpine/alpine regions. To determine the abundance and distribution of bacterial and archaeal ammonia oxidizers in subalpine and alpine forest, three representative forests (primitive Abies faxoniana forest, PF; mixed A. faxoniana and Betula albosinensis forest, MF, and secondary A. faxoniana forest, SF) were selected in the alipine/subalpine region of Western China. Soils were sampled in soil organic layer (OL) due to the sensitive responses to seasonal climate changes. Richness of ammonia oxidizers (ammonia-oxidizing bacteria, AOB; and ammonia-oxidizing archaea, AOA) in soil organic layer were characterized by a real-time quantitative PCR method from targeting on amoA genes, which putatively encode ammonia monooxygenase subunit A. Based on previous investigations, we focused on nine key stages go through three periods as soil temperature varied (1) Growing period: including early growing stage, growing stage, and later growing stage. (2)Freeze period: including early freezing stage, freezing stage, and later frozen stage. (3)Thawing period: including early thawing stage, thawing stage and later thawing stage. Amounts of bacterial and archaeal amoA gene were detected in soil organic layer under three subalpine and alpine forests. The abundance of both bacterial and archaeal amoA showed similar tendency in different key stages, which significantly decreased from growing period to freeze period and then significantly increased, suggesting the strongly effects of temperature fluctuation such as seasonal freeze-thaw cycles. The abundance of bacterial and archaeal amoA gene were the lowest at freeze period, whereas the highest abundance of ammonia-oxidizer was observed at thawing period. Furthermore, the ratio of archaea to bacterial amoA abundance was significantly affected by negative accumulated temperature in all key periods except for later freeze period. Compared with bacterial amoA, higher abundance of archaeal amoA was observed at later freeze stage when soil organic layer was deeply frozen with the highest negative accumulated temperature, although the ratios were varied in different forests at other stages. Except for the early freeze stage, higher abundance of Archaeal amoA was observed compared with bacterial amoA in high altitude forests (PF) due to high negative accumulated temperature. In contrast, the abundance of bacterial amoA was higher than that of archaeal amoA in low altitude forests (SF) except for later freeze stage. The results indicated AOA might have better adaptations in cold environment condition in comparison with AOB, which provide direct evidence for understanding the ecological importance of bacterial and archaeal ammonia-oxidizer in the subalpine and alpine fir forests.