To solve the problem of fluidized bed biofilter in the process of operation with the phenomenon of bed elevation which affects its normal use, a filter media self-cleaning device based on ultrasonic positioning technology was developed and the biofilter was integrated into the scortum barcoo recirculating aquaculture system. The conventional fluidized sand biofilter was used as the control group (CF) and the developed self-cleaning fluidized sand biofilter was used as the experimental group (EF). The degree of bed elevation and media loss in the two groups of fluidized sand biofilter were compared, the removal load on TAN was studied, and the differences in bacterial community structure in different areas of the fluidized sand biofilter were analyzed by high-throughput sequencing. The results showed that the bed height and media loss of the fluidized sand biofilter could be effectively controlled by ultrasonic positioning technology, and the weekly bed height and media loss of the EF group were only 1.8±0.3 cm and 28±12 g at a 150% bed expansion rate, which was 500% and 350% lower than those of the CF group, respectively. The average TAN removal load of the EF group reached 762 ± 164.33 g/(m3·d), which was significantly higher than that of the CF group (P < 0.05). During the rapid degradation of TAN, nitrite nitrogen did not accumulate significantly in both groups, and the dissolved oxygen concentration, alkalinity, and COD concentration in the water were all decreased to some extent. No significant differences in the structure and abundance of bacterial populations between the surface and bottom filter media of the EF group were observed, with the main dominant bacteria including Haliangium, Candidatus_Microthrix, Rhodobacter, and Nitrospira. The differences in the structure and abundance of bacterial populations between the surface and bottom media of the CF group were greater, while the dominant species were relatively similar, with the dominant populations being Romboutsia and Clostridium_sensu_stricto_1. The abundance of Nitrospira was significantly higher in the EF group than in the CF group, suggesting that maintaining the biofilm thickness at a reasonable level may facilitate the enrichment of functional bacteria and thus enhance the nitrification performance of the fluidized sand biofilter.