The parent material is the material basis for soil formation, and the physical and chemical properties of the soil that develops from different parent materials are very different, which affects the community structure of microorganisms in the soil. Currently, research on AOA and AOB is mainly conducted on rice soils in different regions. However, due to the different climatic conditions, cropping patterns, fertiliser systems and rice varieties in different regions, it is difficult to systematically analyse the distribution law and reaction characteristics of the community structure of AOA and AOB. Therefore, relying on the "The Long-term Positioning Experiment of Rice Soil Ex-situ Soil" of the Taoyuan Agricultural Ecology Experimental Station of the Chinese Academy of Sciences. Three rice soils with different parent material were analysed from Yingli in Guangdong Province （YL, latosol）, Yingtan in Jiangxi Province （YT, quaternary red soil） and Taoyuan in Hunan Province （TYG, river alluvium） were selected. The physicochemical properties and nitrification rates of the three soils were measured using conventional agrochemical soil analysis, and the similarities and differences in AOA and AOB gene abundances and community structure were analysed using real-time quantitative PCR and Illumina MiSeq sequencing. Nitrification rate was presented as YT>YL>TYG except at tillering stage. The quantitative results show that the abundance of AOA dominates in YL and YT, with AOA/AOB ratios between 0.72 and 3.05 and 0.98 and 1.52, respectively. In TYG, The abundance of AOB is dominant, with an AOA/AOB ratio between 0.21 and 0.75. Soil parent material has a significant influence on the AOA and AOB community structure. The predominant genera are clear in the AOA, and Nitrosospira in the AOB with three soils. The redundancy analysis （RDA） showed that pH and DOC were the most important factors influencing the AOA and AOB community structure. In conclusion, there are differences in the physicochemical soil properties in paddy soils developed from different parent materials in the same environment, which affects the abundance and community structure of AOA and AOB.