Pacific saury ( Cololabis saira) is usually sold as whole fish in wholesale markets, or in its gutted form which is easy for consumers to cook in retail markets. In order to assess the effect of gutting on the shelf life of Pacific saury during refrigerated storage and reveal the microbial community, fish samples grouped into (I) whole fish and (II) gutted fish were analyzed periodically for sensory, biochemical and microbiological characteristics, and high-throughput sequencing technology was used to investigate the microbiota. Results showed that the sensory score for the gutted fish became unacceptable on day 8, while the whole fish score remained acceptable for 10 days. The total volatile basic nitrogen (TVB-N) value of the gutted fish reached 30 mg N (100g) –1 on day 6, while that of the whole samples surpassed 30 mgN(100g) –1 on day 10. The thiobarbituric acid reactive substances (TBARS) value of the gutted fish got close to 5.0 mg kg –1 on day 10, while that of the whole samples surpassed 5.0 mg kg –1 on day 14. The aerobic plate colony counts (APCs) for the gutted and whole Pacific saury reached 7.0 log10 CFUg –1 on days 6 and 10, respectively. Organoleptic, biochemical and microbiological analyses revealed that shelf-lives should be 6–8 days for gutted fish and 10 days for whole fish. Microbiota analysis results showed that gutting partly changed the initial microbiota, but didn’t alter the dominant bacteria during storage. When the fish were spoiled, high proportion of Pseudomonadaceae was detected in both groups.