Water scarcity and soil salinization constrain cotton production in arid regions, yet the joint effects of irrigation and plastic-film mulching on soil hydrothermal–salinity dynamics, dry matter partitioning, yield, and water productivity remain unclear. A two-year field experiment combined three irrigation amounts (3360, 4200, and 5040 m³ ha⁻¹; W1–W3) with plastic-film mulching (M1) and non-mulched (M0) treatments. Mulching increased soil water content by 7.23–32.76% during flowering and boll setting and shifted dry matter allocation toward reproductive organs, increasing the proportion allocated to reproductive organs by 6.43–11.16%. Irrigation markedly altered soil salinity distribution, with W2 promoting relative salt accumulation at 80–100 cm, whereas W3 maintained lower ECe across the 0–100 cm profile. W3M1 consistently produced the highest seed cotton yield, while W2M1 achieved the highest water productivity and maintained 89.4% of the two-year mean yield of W3M1 with 16.7% less irrigation. Path analysis further showed that yield variation was associated primarily with reproductive-organ dry matter rather than vegetative biomass or the integrated soil hydrothermal–salinity condition (path coefficient = 0.870, p < 0.001). These findings support irrigation strategies tailored to water availability and production goals while balancing yield, water use, and salinity risk in arid cotton systems.