The accurate estimation of aboveground biomass (AGB) is essential for monitoring crop growth and supporting precision agriculture. Traditional AGB estimation methods relying on single spectral indices (SIs) or statistical models often fail to address the complexity of vertical canopy stratification and growth dynamics due to spectral saturation effects and oversimplified structural representations. In this study, a unmanned aerial vehicle (UAV) equipped with a 10-channel multispectral sensor was used to collect spectral reflectance data at different growth stages of cotton. By integrating multiple vegetation indices (VIs) with three algorithms, including random forest (RF), linear regression (LR), and support vector machine (SVM), we developed a novel stratified biomass estimation model. The results revealed distinct spectral reflectance characteristics across the upper, middle, and lower canopy layers, with upper-layer biomass models exhibiting superior accuracy, particularly during the middle and late growth stages. The coefficient of determination of the UAV-based hierarchical model (R² = 0.53–0.70, RMSE = 1.50–2.96) was better than that of the whole plant model (R² = 0.24–0.34, RMSE = 3.91–13.85), with a significantly higher R² and a significantly lower root mean squared error (RMSE). This study provides a cost-effective and reliable approach for UAV-based AGB estimation, addressing limitations in traditional methods and offering practical significance for improving crop management in precision agriculture.

Long-term continuous cropping in cotton fields of Southern Xinjiang has limited crop productivity. To investigate how subsoiling depth regulates ecosystem-level water partitioning and thereby enhances water productivity mechanisms, a two-year field experiment was conducted in a mulched drip irrigation cotton field in Southern Xinjiang. Using a non-subsoiled field in the current season (CT) as the control, three subsoiling depths were established: subsoiling at 30 cm (ST1), 40 cm (ST2), and 50 cm (ST3). Changes in evapotranspiration partitioning and water use efficiency were analyzed. The results showed that subsoiling enhanced the utilization of deep soil water. Compared with CT, the ST2 and ST3 treatments significantly reduced soil water storage in the 0–60 cm layer during the flower opening to boll-setting stages, while soil water consumption increased by 26.4 mm and 28.8 mm, respectively. We demonstrate that subsoiling depth exerts a predominant control on the partitioning of evapotranspiration. Increasing subsoiling depth systematically shifted water loss from non-productive soil evaporation to productive plant transpiration, with the ST2 and ST3 treatments decreasing seasonal soil evaporation by 24.1% and 25.1%, respectively, and increasing plant transpiration by 21.9% and 22.8%, and lowering the Es/ET (where Es is soil evaporation and ET is evapotranspiration) ratio by 22.1% and 27.1%. However, this maximal physiological water-saving did not yield the optimal agronomic return. We established a non-linear relationship in which the ST2 treatment uniquely achieved the maximum seed cotton yield, WUE (water use efficiency), and IWUE (irrigation water use efficiency) (increasing by up to 34.4%, 17.2%, and 23.4%, respectively). This optimal depth better balances water resource allocation and reproductive growth. We conclude that under sandy loam soil conditions in typical mulched drip-irrigated cotton areas of Southern Xinjiang, implementing an optimal subsoiling depth (40 cm) can engineer a more resilient soil–plant–water continuum, providing a feasible pathway toward enhancing water and crop production sustainability.