Soil salinization severely constrains cotton (Gossypium hirsutum L.) productivity in arid irrigated regions, while prolonged shallow drip irrigation exacerbates root superficialization and limits deep soil water utilization. However, the mechanistic pathways by which coupled water-organic management regulates root system architecture (RSA) plasticity and the optimal coupling parameters remain inadequately quantified. A two-year (2022–2023) field experiment was conducted in Alar, Xinjiang, China, to investigate coupling effects of three deficit irrigation regimes (W1, W2 and W3, targeting 90%, 75% and 60% of seasonal non-stressed crop evapotranspiration, ETc) and four soil amendments (CK: chemical fertilizer; T1: biochar 4.5 t ha⁻¹; T2: potassium humate 150 kg ha⁻¹; T3: bio-organic fertilizer—composted sheep manure plus wheat straw inoculated with a salt-tolerant Bacillus subtilis strain—3.0 t ha⁻¹) on cotton RSA using integrated shovelomics and minirhizotron phenotyping. Results demonstrated that the W2 ×T3 treatment was associated with optimized RSA, showing increased deep root length density (40–80 cm) by 37.5% (from 0.48 to 0.66 cm cm⁻³) and reduced fine root turnover rate by 27.9% (from 2.47 to 1.78 year⁻¹) compared to W1 ×CK. This "steep and deep" architecture coincided with 47.2% higher root hydraulic conductivity (3.21 × 10⁻⁴ vs. 2.18 × 10⁻⁴ kg s⁻¹ MPa⁻¹ m⁻²). Structural equation modeling revealed strong associations between amendment-induced rhizosphere improvements—including 34.0% reduced Na⁺/K⁺ ratio and 50.0% increased aggregate stability—and root deepening (path coefficient β = 0.54), which showed the strongest association with yield (β = 0.59). Random forest analysis corroborated that deep rooting index (31.2% relative importance), rhizosphere Na⁺/K⁺ ratio (18.7%), and root hydraulic conductivity (13.4%) were the top yield-associated variables, whereas total root biomass ranked last of the twelve predictors (1.1%). The W2 ×T3 treatment achieved 15.3% higher seed cotton yield (5847 vs. 5072 kg ha⁻¹), 33.7% higher irrigation water productivity (WP_I, 1.31 vs. 0.98 kg m⁻³) and 19.6% higher crop water productivity referenced to measured actual crop evapotranspiration (WP_ET, 1.10 vs. 0.92 kg m⁻³), with 13.8% water savings. This study identified W2 ×T3 (75% ETc target + 3.0 t ha⁻¹ bio-organic fertilizer) as the optimal strategy for sustainable cotton production in arid saline-sodic soils.