<p>Salinity remains a critical constraint to the productivity of ‘RD6’, Thailand’s premier glutinous rice cultivar. While the introgression of the <i>Saltol</i> QTL offers a solution, achieving a balance between salt resilience and the preservation of the elite ‘RD6’ metabolic phenotype is essential. This study employed an integrative approach, combining physiological characterization with untargeted metabolomics to evaluate two new introgression lines, Morkho60 − 2 and BC₄F₄ 132-12-61, under reproductive-stage salinity. Physiological assessments indicated that while salt stress impacted photosynthetic machinery across all genotypes, total grain weight remained stable in BC₄F₄ 132-12-61, whereas the susceptible parent ‘RD6’ suffered significant yield loss. The resilience of BC₄F₄ 132-12-61 was driven by superior ion exclusion and enhanced antioxidant enzyme kinetics, which mitigated oxidative damage and maintained spikelet fertility. Crucially, metabolomic profiling demonstrated that BC₄F₄ 132-12-61 maintains a high degree of metabolic stability. Despite achieving physiological tolerance comparable to the donor parent ‘Pokkali’, its global metabolic signature remained tightly clustered with the recurrent parent ‘RD6’. This metabolic isogenicity suggests that the introgression successfully conferred stress-adaptive plasticity without disrupting the fundamental metabolism that defines the ‘RD6’ quality profile. Our findings highlight that BC₄F₄ 132-12-61 achieves a synergistic combination of donor-derived physiological resilience alongside recurrent-parent metabolic traits, marking it as a robust candidate for sustainable cultivation in salt-affected regions.</p>