<p>Cadmium (Cd²⁺) contamination threatens plant viability and human health by disrupting cellular homeostasis and metabolic processes. Investigating the molecular mechanism underlying Cd²⁺ tolerance in plants is necessary to remediate Cd²⁺-contaminated soil. This study presents an integrated physiological, metabolomic, and transcriptomic analysis of the roots, stems, and leaves in response to Cd²⁺ stress. The study found that Cd²⁺ accumulation was significantly lower in Cd²⁺-tolerant cotton. Under 4&#xa0;mM Cd²⁺ stress, the Cd²⁺ content in cotton increased significantly, accompanied by elevated levels of malondialdehyde (MDA), proline (Pro), and hydrogen peroxide (H₂O₂), as well as noticeable damage to the cellular ultrastructure. Metabolomic profiling analysis revealed that Cd²⁺ stress significantly affected the distribution of lipids, amino acids, and organic acids in different tissues. The metabolic pathways of alanine, aspartate, and glutamate are closely associated with Cd²⁺ stress, and the induced elevation of GABA levels plays a crucial role in cotton’s adaptation to Cd²⁺ stress. Exogenous GABA application significantly enhances Cd²⁺ tolerance in cotton by reducing Cd²⁺ accumulation and decreasing the content of Pro, MDA, and H₂O₂. Silencing of the γ-aminobutyric acid (GABA) biosynthetic gene glutamate decarboxylase (<i>GhGAD6</i>) resulted in increased Cd²⁺ sensitivity, demonstrating that GABA alleviates Cd²⁺ toxicity in cotton through reducing Cd²⁺ accumulation and scavenging ROS. These findings elucidate the molecular basis of Cd²⁺ stress tolerance in plants and provide a key for the effective strategy of enhancing Cd²⁺ tolerance in cotton.</p>