In this paper, high-throughput sequencing was used to analyze the diversity of water flora in the biofloc system during nitrogen transformation. A control group and a test group were set in the test. The control group had clean and disinfected seawater, and the test group was a biofloc group. The test period was 30 days. The results show that in the test group, the mass concentration of ammonia nitrogen reached its maximum (2.99 mg/L) on day 5 and then decreased to 0 mg/L; in the control group, the mass concentration reached its maximum (7.51 mg/L) on day 9 and then decreased to 0 mg/L. In the test group, the mass concentration of nitrite nitrogen reached its maximum (12.54 mg/L) on day 17 and then decreased to 0 mg/L; in the control group, it showed a rising trend during the test period and reached 13.42 mg/L on day 30. The mass concentration of nitrate nitrogen in the test group was higher than that in the control group, reaching 19.56 and 6.31 mg/L respectively on day 30. The biofloc system was obviously able to remove ammonia nitrogen and nitrite nitrogen, and the nitrogen transformation rate of the test group was higher than that of the control group. High-throughput sequencing showed that the flora abundance and diversity index of the microorganisms in the biofloc system increased significantly with the increase of the breeding cycle, and the differences were significant in different periods. During the test period, a total of 23 phylum and 549 genera were identified. At the phylum level, the relative abundance of Proteobacteria decreased with time (from 67.72% to 44.45%), while that of Bacteroidetes and Chloroflexi increased with time (respectively from 5.99% and 6.68% to 16.06% and 19.02%). The main bacteria related to nitrogen transformation included Ardenscatena and Nitrospiraceae, whose relative abundance increased with time (respectively from 0.34% and 0.07% to 12.69% and 0.2%), while that of Nitrosopumilus decreased with time. The function and microbial diversity of the biofloc system showed significant changes during the breeding cycle. This study has reference value for improving the utilization efficiency of the biofloc system breeding mode.