Secondary salinization in mulched drip-irrigated cotton fields of arid oasis-desert transition zones in Xinjiang imposes coupled root-zone constraints, including salt-induced aggregate structural degradation and ionic stress. However, field evidence remains limited on whether integrating a structure-oriented soil conditioner with humic acid can generate stable improvements across growing seasons. A two-year field experiment with a randomized block design (three replicates) was conducted to evaluate four treatments: control (CK), polyacrylamide (PAM, 30 kg ha(-1)), humic acid (HA, 450 kg ha(-1)), and PAM + HA. Soil physical and chemical properties and aggregate-size distribution were determined after harvest, while enzyme activities and root traits were assessed at the flowering-boll stage. Structural equation modeling (SEM) and random forest (RF) analysis were used to explore soil-root-yield linkages and identify key soil predictors associated with yield variation. Treatment effects were most evident in the 0-20 cm layer, with PAM + HA showing the greatest overall improvement. In the topsoil, PAM + HA lowered soil pH from 8.35 to 7.88 in 2024 (p < 0.05), increased soil organic carbon (SOC) to 4.29 g kg-1 in 2025 (p < 0.01), and increased NO3--N to 25.51 and 30.27 mg kg(-1) in 2024 and 2025, respectively (both p < 0.05). PAM + HA also enhanced cellulase activity from 6.17 to 16.85 mg glucose g(-1) 72 h(-1) in 2024 and increased seed cotton yield to 6683.69 and 5996.89 kg ha(-1) in 2024 and 2025, with a 51.0% yield increase over CK in 2024. SEM showed that root development had the strongest direct positive effect on yield (beta = 0.79, R-2 = 0.63; goodness of fit (GOF) = 0.74), while random forest identified alkaline phosphatase, cellulase, and NO3--N as the main yield predictors (out-of-bag R-2 (OOB R-2) = 0.672, p = 0.01). This study elucidated the effects of the combined application of a structure-oriented soil conditioner and humic acid on the root-zone environment of mulched drip-irrigated cotton fields in arid regions, providing a theoretical basis for the coordinated regulation of soil structural improvement and nutrient activation in saline-sodic cotton fields.