The cotton growing area in southern Xinjiang is facing the combined stress of fresh water shortage, soil salinization and seasonal drought, and the safe and efficient utilization technology of brackish water is urgently needed. To elucidate the mechanism by which brackish water supplementary irrigation affects canopy photosynthesis and yield of cotton in southern Xinjiang, using cultivar ‘Xinluzhong 88’ as the test material, three treatments were established: conventional irrigation (CK), brackish water supplementary irrigation+ subsoiling (SWS), and brackish water supplementary irrigation+ subsoiling+ soil conditioner (SWST). The effects of these treatments on leaf area index (LAI), chlorophyll content (SPAD), canopy interception rate (FIPAR), net photosynthetic rate (Pn), transpiration rate (Tr), stomatal conductance (Gs), intercellular CO₂ concentration (Ci), dry-matter accumulation, and seed-cotton yield were investigated. SWST produced the highest LAI and SPAD at both budding and boll-opening stages, increasing LAI by 30.39% and SPAD by 14.63% compared with CK. The interception rate showed an increasing trend with cotton growth. The interception rate of SWST during the fluffing stage reached 0.95 at a vertical height of 60-70 cm. This treatment sustained high photosynthetic efficiency and stimulated dry-matter accumulation, thereby boosting yield. During the bud stage and floret stage, the levels of Tr, Pn and Gs in SWST-treated samples were significantly higher than those in CK-treated samples, with no significant difference observed between SWST and SWS treatments (P<0.05). The water use efficiency (WUEi) of SWST was 11.4% higher than that of CK, while the carbon uptake (Ci) decreased by 6.29%. Dry-matter accumulation entered the rapid phase 5 days earlier in SWST than in CK, resulting in an 18.42% yield increase and the highest growth characteristic value (88.71). Supplemental irrigation with brackish water at a mineralization degree of 4.5 g/L, combined with deep loosening and the application of a soil conditioner, significantly increased cotton LAI, SPAD values and WUEi, optimized canopy structure, increased the interception rate of cotton populations while enhancing dry matter accumulation, finally producing the highest seed-cotton yield of 7557.65 kg/hm². In the future, multi-year positioning and different salinity gradient tests can be carried out to improve the regional adaptation technology model.