Increasing evidence revealed that ammonia oxidation Archaea (AOA) belonging to Thaumarchaeota could control nitrification in various agricultural ecosystems. Studying the impact of different long-term fertilization systems on the shift of the AOA community structure and vertical distribution would contribute to understanding the soil nutrient biogeochemical cycles and microbial drive mechanisms. In the present study, an "N, P, K long-term fertilization field experiment (1982-2014)" was established in a Calcareous Purple Paddy soil in Suining City, Sichuan Province of the PR China. Eight treatments including three chemical fertilizer (CF) treatments (N, NP, and NPK), three CF plus farmyard manure (M) treatments (NM, NPM, and NPKM), M only, and no fertilizer (CK) as control were used. Soil samples amended with different long-term fertilization systems at four different depths (0-20, 20-40, 40-60, 60-90 cm) were collected; the soil physico-chemical parameters and the shift of the AOA community structure and vertical distribution were analyzed by chemical analysis and denaturing gradient gel electrophoresis (DGGE). The results showed that compared to the no fertilizer treatment (CK), soil pH decreased under the CF treatments, and showed little variation under CFM treatments. The pH values in the 0-20 cm soil depth were lower than those in other soil depths. The combined use of farmyard manure and chemical fertilizer could also improve the soil total nitrogen concentration. The total nitrogen content in 0-20 cm soil depth was also higher than that of other depths. Fertilizer increased the soil ammonia content in the 0-20 cm soil depth, and in this soil depth, the CK treatment had the lowest ammonia concentration. Furthermore, soil ammonia concentrations under the four CFM fertilizer treatments (e.g. M, NM, NPM, and NPKM) were similar. Additionally, chemical fertilizer plus farmyard manure decreased the soil nitrate concentration, and the nitrate concentration in the 0-20 cm soil depth was higher than that of other depths. Based on the DGGE analysis, different fertilization systems affected the AOA community structure in different soil depths differently. The AOA community structure in the 0-20 cm depth with different fertilizer amendments showed minor variation. With increasing soil depth, the AOA community structure with different fertilization systems varied significantly. The AOA community structure in the CK and N fertilized soil were much simpler than those under CF and CFM fertilizer treatments. However, the AOA community structure showed significant vertical variation, both the richness and Shannon-Wiener diversity index in the 0-20 cm soil depth were the highest, while those in the 60-90 cm soil depth were the lowest. According to the sequence and phylogeny analysis, AOA in Calcareous Purple Paddy soil were all affiliated to Thaumarchaeota, and they were highly similar to the AOA in different soil and water environments. According to the redundancy gradient analysis (RDA), four soil physico-chemical parameters such as pH, total nitrogen, ammonia, and nitrate concentration showed 11.3, 2.8, 1.8, and 1% contributions to the AOA community structure, respectively. Soil pH (P=0.012) was the critical factor to shape the AOA community structure in Calcareous Purple Paddy soil. The study revealed that AOA in the Calcareous Purple Paddy soil responded to the fertilization systems variously, and showed an obvious vertical distribution.