Introduction: Halophyte-based intercropping may involve root interactions beyond desalinization in alleviating salt stress in glycophytes. Methods: To elucidate the mechanisms of root interactions enhancing soybean ( Glycine max ) salt tolerance intercropping with Suaeda salsa , we analyzed rhizosphere metabolomes and bacterial communities under two salt treatments (no additional NaCl, S1; 3 g kg ^–1 NaCl, S3) and three root interaction modes: (1) plastic barrier (no root interactions), (2) nylon mesh barrier (root interactions only), and (3) no barrier (root interactions with potential salt redistribution). Results: Both NL and NS significantly increased soybean biomass compared with PL under both salt treatments, with no significant difference between NL and NS. Under S3, NL increased soybean biomass by 80% relative to PL without significantly changing soil electrical conductivity, accompanied by increases in rhizosphere carbohydrates, organic acids, betaine, flavonoids, and putative plant growth-promoting bacteria (PGPB). Although soybean rhizosphere Na ⁺ decreased under NS compared with PL and NL, this was accompanied by reduced putative PGPB abundance and no further biomass increase compared with NL. Coumestrol, trehalose-6-phosphate, and isopentenyl pyrophosphate (IPP) were identified as hub metabolites associated with soybean rhizosphere microbial community structure, with the IPP-related module representing a potential component of the salt-response network. Intercropping also increased available phosphorus (AP) in both species’ rhizospheres, with increases in soybean associated with organic acids and those in S. salsa associated with rhizosphere pH shifts and putative PGPB changes. Discussion: These findings indicate that root interactions enrich salt−tolerance−related metabolites in the soybean rhizosphere and suggest potential metabolic-microbial coupling underlying intercropping−induced salt tolerance.

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