Microbial co-metabolism can effectively degrade the polycyclic aromatic hydrocarbons (PAHs) in polluted sediment of river. The salinity of overlying water in tide river section at the junction of inland and outland water in coastal cities fluctuates greatly due to tidal influence, but the effect of salinity fluctuation on the co-metabolism degradation of PAHs in the sediment and the response of microbial community are still unclear. In this study, sodium acetate and phthalic acid were used as co-metabolic carbon sources to investigate the effect of fluctuation with a range of 0-50‰ salinity of overlying water on the degradation of PAHs in the sediment, monitor the changes of the physicochemical properties and sulfide content of the sediment, and analyze the changes of the microbial community in the sediment under the condition of salinity fluctuation. The results showed that a low-salt environment (0-20‰) was more conducive to co-metabolism and degradation of PAHs, and the degradation rate of PAHs was 1.5-3.3 times higher than that of a high-salt environment (>20‰-50‰). Moreover, the high osmotic pressure produced by the high-salt environment would affect the microbial activity and inhibit the co-metabolism reaction, resulting in a slow decline in pH and oxidation-reduction potential (ORP) of the sediment and a decrease in the reduction rate of SO^2-₄. High-throughput sequencing showed that salinity fluctuation could significantly change the microbial community structure of the sediment. Proteobacteria, Firmicutes, and Bacteroides were dominant in the low-salt environment while Marinobacterium and Marinobacter were the dominant genera involved in the co-metabolism and degradation of PAHs. In addition, the stress effect of the high-salt environment inhibited the activity of most microorganisms, while the abundance of Desulfobacter and Chloroflexi continued to increase, and SBR1031 and Sulfurovum became the dominant bacteria.