Phascolosoma esculenta ( P. esculenta ) is a benthic marine invertebrate endemic to China, and abrupt salinity shifts in aquaculture environment often cause mass mortality. In this study, individuals were divided into three salinity treatments: S20 (salinity 20), S10 (salinity 10), and S6 (salinity 6). Histological examination, enzyme activity assays, gut microbiota 16S rRNA sequencing, and transcriptome profiling were integrated to comprehensively evaluate intestinal responses to low‐salinity stress. After 30 days exposure, low‐salinity induced pronounced intestinal injury, including thinning of the mucosal layer (ML), villus collapse, and inflammatory cell infiltration. Malondialdehyde (MDA) concentrations showed a gradual elevation across groups (S20, S10, and S6), rising from 2.91 to 4.97 nmol/mg prot. Glutathione peroxidase (GSH‐PX) activity peaked at 37.23 U/mg prot in the S10, compared with 25.19 U/mg prot in the S20 and 29.36 U/mg prot in the S6, indicating activation of antioxidant defenses under moderate stress but exhaustion under severe stress. Acid phosphatase (ACP) activity declined from 4.32 U/mg prot (S20) to 3.99 U/mg prot (S10) and 3.02 U/mg prot (S6). Similarly, alkaline phosphatase (AKP) activity dropped from 1.33 U/mg prot (S20) to 1.03 U/mg prot (S6), reflecting suppressed immune function. Gut microbiota analysis showed significantly reduced Shannon diversity in the S6, with community composition shifting from Firmicutes/Bacteroidota toward Proteobacteria. Transcriptome analysis identified 125, 364, and 413 differentially expressed genes (DEGs) in the S10 vs. S20, S6 vs. S20, and S6 vs. S10 comparisons, respectively, which were primarily enriched in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways such as TNF signaling, RIG‐I‐like receptor signaling, and osteoclast differentiation. In summary, P. esculenta can maintain homeostasis by activating the antioxidant system under moderate low‐salinity stress. However, under severe low‐salinity conditions, it exhibits activated inflammatory responses, reprogrammed amino acid metabolism, and excessive activation of apoptosis, ultimately leading to severe damage to the intestinal barrier. This study elucidates the salinity tolerance mechanisms of this species from an omics perspective, providing important insights for its healthy aquaculture and selective breeding for salinity tolerance.