The study aims to analyze the changes of microbial community on the surface of mackerel (scomber japonicus) during different frozen storage, to provide relevant basis for microbial safety control during frozen storage of mackerels. The fresh mackerels were stored in the refrigerator at -18 °C, and samples were taken on the 0th day, 40th day, and 100th day, and then the surface microorganisms were extracted and analyzed by high-throughput sequencing technology. The number of operational taxonomic units (OTU) for frozen mackerels ranged from 115 to 266, with an optimized effective sequence of 38 899 to 45 012. Among them, the OTU number of frozen mackerels on day 0 was the highest, while the OTU number on day 100 was the lowest. At the end of freezing, the average values of the three indicators of Ace, Chao, and Shannon of the sample were low, but the Simpson index was high, showing low species and abundance of the flora. Meanwhile, psychrobacter and sphingomnnas were the dominant flora at the 0th day of the samples, and acinetobacter also became the main microorganisms at the 40th day of the samples. When the samples were frozen for 100 days, the dominant flora was lactococcus and bacillus. The composition of the microbiota of mackerels at different periods of frozen storage is quite different, indicating that the frozen storage time has a significant impact on the composition of the microbiota.