To study the vertical distribution of archaea in the world’s deepest blue hole Yongle Blue Hole (YLLD), and its distribution characters driven by nitrogen, as well as, to predict the ecological functions of archaea, we collected 12 seawater samples from depths of 2 m to 170 m. Illumina high-throughput sequencing was performed, and the results indicated that the abundance of Thaumarchaeota (44.34 %) was the highest, and the dominant community of archaea at different water depths (surface, middle, and bottom) was different. The diversity of archaeal communities was greater in the surface and deep layers of the YLLD than in the middle layer, with significantly higher diversity in the deep layer than in the middle layer (P < 0.05). The results of the redundancy analysis showed that nitrate and ammonia nitrogen significantly influenced the structure of the seawater archaeal community at different depths (P < 0.05). By means of bioinformatics predicted that archaea play an important role in the aerobic ammonia oxidation in the ecosystem found within YLLD. The findings of this study showed that nitrate and ammonia were the main environmental factors affecting archaeal communities in different water layers of YLLD, Aerobic ammonia oxidation and nitrification were their primary ecological functions. These findings laid the theoretical foundation for further research on microbial biogeochemical processes in extreme environments, such as blue holes.