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 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 (GhGAD6) 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.