Root systems are pivotal for nutrient absorption, exhibiting high plasticity in phosphorus (P) acquisition, and significantly influencing soil phosphorus availability. However, the impacts of different P application methods on root parameters and P utilization efficiency in cotton (Gossypium hirsutum L.) under Xinjiang conditions are still not well understood. To identify optimal P fertilization strategies, a consecutive two-year field experiment (2023-2024) under mulched drip irrigation was conducted. Three P application methods were tested: no P (CK), basal P application (PB), and drip P application (PD). Results revealed that P application methods significantly affected cotton dry matter, P use efficiency, root morphology, and yield (p < 0.05). Over the two years, the optimized treatment (25% P applied at bud stage and 25% at flowering-boll stage, PD) increased yield by 13.62% and 9.50% compared to full basal application (PB), with P use efficiency improved by 22.04-31.51% and agronomic efficiency improved by 6.56-9.75 kg kg(-1). PB significantly increased soil-available P in 0-20 cm (34.17-70.09%) and 20-40 cm layers (30.37-70.32%) compared to CK. During the bud stage, PD treatment exhibited higher soil-available P in the 20-40 cm layer than PB. PD enhanced P uptake and dry matter accumulation, with increases of 22.43-36.33% and 7.90-15.55% in reproductive organ P accumulation compared to other treatments. Root parameters followed PD > PB > CK across all treatments. At the seedling stage, PB increased total root length by 19.79% compared to CK, while PD increased root volume by 46.15% compared to PB. During the bud stage, PB increased root volume by 53.33% compared to CK, and PD enhanced root surface area and volume by 39.25% and 47.82% compared to PB. Root volume showed a significant positive correlation with phosphorus absorption across growth stages. The PD treatment significantly enhanced soil P availability and P use efficiency and optimized root spatial distribution. This treatment consistently increased cotton yield by 30.41-39.09% (p < 0.05) compared to CK, demonstrating stable positive effects. This study highlights that adjusting P application methods can establish sustainable, high-yield agricultural fertilization systems.