Abstract Optimising the root hydraulic architecture, which is defined by the integration of morphological and hydraulic traits, plays a crucial role in enhancing the drought tolerance of crops. However, the mechanisms by which root hydraulic architecture coordinates structural and functional adaptations under drought remain unclear. In this study, we used paper‐based cultured 13 cotton cultivars under no‐stressed and drought‐stressed conditions, and identified a drought‐tolerant (Guoxin 02) and a drought‐sensitive (Ji 228) cultivar. The drought‐tolerant cultivar exhibited enhanced root hydraulic conductance (Lpr) through increased lateral root length and number, reduced lateral root tip angle, and lower root width/depth ratio. Anatomically, drought tolerance was associated with narrower xylem vessels to limit axial conductance ( K x ) and reduced cortex cell layers to increase radial hydraulic conductance ( K ox ), thereby balancing hydraulic efficiency and embolism resistance. Despite lower K x , the high root hydraulic conductance ( K root ) in the drought‐tolerant cultivar was maintained by lateral root proliferation, demonstrating a synergistic interplay between morphology and hydraulics. These findings highlight the plasticity of root hydraulic architecture as a key target for breeding drought‐resilient cotton.