Background and aims: Crop breeding for greater yield has indirectly modified plant anatomical traits, yet the relationships between these traits and yield improvement remain poorly understood, particularly in dryland wheat. This study aimed to investigate associations between key root and leaf anatomical traits and grain yield in winter wheat cultivars grown under rainfed conditions. Methods: Field experiments were conducted at two dryland sites in Gansu Province, northwest China (Dingxi and Pingliang), using 20 and 18 winter wheat cultivars, respectively. Seminal root and flag leaf samples were collected at the elongation and anthesis stages. Anatomical traits-including root xylem area, cortex area, root respiration, leaf vein density, leaf vein ratio, stomatal length, and stomatal density-were measured using light microscopy, scanning electron microscopy, and image analysis. Grain yield was determined at maturity. Regression analyses and structural equation modeling were used to examine trait-yield relationships. Results: Grain yield was significantly and positively correlated with seminal root xylem area at anthesis at both sites (p < 0.05). In Pingliang, root respiration was negatively correlated with yield (p < 0.05) and positively correlated with root cortex area (p < 0.05) at anthesis. No significant relationships were detected between yield and leaf vein traits, leaf thickness, or photosynthetic parameters. Yield was negatively correlated with stomatal length on both leaf surfaces (p < 0.05) and positively correlated with abaxial stomatal density (p < 0.05) in Pingliang. Stomatal length, index, and density were all greater on adaxial than abaxial surfaces (p < 0.01), and stomatal length was negatively correlated with stomatal density across both growth stages (p < 0.05). Structural equation modeling revealed that root xylem area exerted a positive direct effect on yield, while root respiration and abaxial stomatal length had negative direct effects. Conclusions: Larger seminal root xylem area, reduced root cortex area with less respiration, and smaller but more numerous abaxial stomata are key anatomical traits associated with greater grain yield in dryland wheat. Below-ground and above-ground anatomical traits are coordinated to optimize yield formation under water-limited conditions. These findings provide potential selection targets for wheat breeding programs aiming to enhance yield stability in dry environments.