[Objective] Nitrification is a critical process of the nitrogen cycle which is driven by ammonia-oxidizing archaea (AOA) and bacteria (AOB). It has been observed that long-term fertilization affect soil properties and nitrifying microbial community in paddy soils. However, the effect of long-term fertilization on the community structure of AOA and AOB along the depth in paddy soils has been given little attention.[Method] From a long-term experiment on fertilization management of a paddy field in Ningxiang, Hunan Province, we selected four treatments; no fertilization (CK), straw organic fertilizer (ST), organic-inorganic fertilizer (OM), and inorganic fertilizer (NPK), and used real-time fluorescent quantitative PCR and Illumina MiSeq sequencing technology to analyze the soil properties, and abundance and composition of AOA and AOB in the soil layers (0-10 cm, 10-20 cm, 20-30 cm, 30-40 cm).[Result] ST, OM and NPK treatments increased the contents of soil organic carbon, total nitrogen, available phosphorus and the nitrification potential in each soil layer, but decreased soil pH. The contents of soil organic carbon, total nitrogen, alkali hydrolyzable nitrogen, available phosphorus, and the nitrification potential decreased with an increase in soil depth, while the pH value showed an opposite trend. Importantly, NPK had a more significant effect on soil acidification (0-20 cm) compared to the other fertilizers. The AOB abundance in the control (no fertilization) treatment was higher than AOA abundance, with the ratio of AOB/AOA abundance in the range 9.24-29.19. Also, the application of fertilizers promoted the growth of AOA, with the AOA/AOB abundance ratio in the range 0.77-31.28. Long term application of fertilizers enriched the proportion of Nitrosocosmicus in AOA population and Nitrosolobus in AOB population. Redundancy analysis showed that available phosphorus and pH had a significant impact on the composition of AOA and AOB communities, with interpretive degrees of 31.5% and 46.7%, respectively. This indicated that available phosphorus and pH were the key factors driving the succession of AOA and AOB community structure. Additionally, the vertical distribution characteristics of AOA and AOB were affected by different fertilization measures and soil layers.[Conclusion] Long term fertilization can acidify paddy soil and change the main executor of ammonia oxidation in the nitrification process. Variations in carbon, nitrogen, phosphorus and pH along the paddy soil depth induced the observed changes in AOA and AOB abundance and community composition and then affected the nitrification ability of soil. This study can serve as a theoretical basis for improving nitrogen use efficiency and reducing greenhouse gas emission.