Drought stress is the primary limiting factor for establishing woody seedlings in semi-arid Zagros ecosystems, reducing root efficiency and threatening restoration success. This study examined the combined effects of Glomus mosseae and Multi-Walled Carbon Nanotubes (MWCNTs) on the root morphological and structural traits of Cercis siliquastrum seedlings under drought conditions. Treatments were arranged in a completely randomized design (CRD) with a 3×2×3 factorial structure and three replications per treatment combination, including three drought levels (100%, 60%, 20% FC), two fungus levels (inoculated/uninoculated), and three MWCNT levels (0, 50, 100 mg L⁻¹). Significant interactions (p<0.01) were observed for stress × fungus on root tissue diameter and density, and for stress × fungus × MWCNTs on root tissue density. Under severe stress (20%), root volume, fresh weight, dry weight, and length decreased by 71%, 68%, 65%, and 26%, respectively. Fungal inoculation increased these parameters: volume (49%), fresh weight (48%), dry weight (39%), and length (16%). MWCNTs at 100 mg L⁻¹ improved dry weight (52%), fresh weight (38%), volume (27%), and length (21%). The combined application of fungus and MWCNTs enhanced seedling growth by improving root uptake efficiency, offering a promising strategy for Zagros forest restoration under drought conditions.