Abstract: Scientific management and properly utilization of sediment is of significance for healthy aquaculture and resource utilization in long-term culture ponds. Rotation of pond culture and cultivation appropriately is an effective way, which can reuse the nutrients in sediments and improve the sediment environment. Nine ponds with the same basic conditions were suspended aquaculture activities and used for the experiment of rice substrate improvement. Empty pond was used as the control (CK), two treatments were set: planting rice without field drying (T1) and planting rice with field drying group (T2). The main chemical properties and abundance of ammoxidation archaea in the sediments during rice growth were determined, and the community diversity and structure difference of AOA in rice after harvest were determined. The results showed that, compared with CK, the TN, TP and OM in sediments of T1 (or T2) decreased significantly by 26.58% (31.04%), 58.84% (58.38%) and 11.17% (16.11%) respectively. Compared with T1 and T2, it was concluded that the degradation of TP and OM in sediment was accelerated by solarization. The nitrification intensity and the abundance of AOA in the sediments increased at first and then decreased. Compared with CK, the nitrification intensity of T1 and T2 was significantly increased at tillering stage and jointing stage, while the abundance of AOA was significantly increased at tillering stage. Diversity index and OUT number of AOA in sediments were increased and a large amount of new AOA populations generated by rice cultiviton. The increased species in T1 was Candidatus nitrosocosmicus cluster (3.84% of the total sequence), and which in T2 was Candidatus nitrosotenuis cluster (3.24% of the total sequence). It indicated that rice planting can effectively alleviate the nutrient enrichment in pond sediments, which can be used as a supporting measure for sustainable pond aquaculture.