Lead (Pb) and nickel (Ni) are serious soil pollutants that adversely affect plant growth and development and need to be removed through phytoremediation. The present study aimed to assess the morphological indices of Albizia lebbeck (L.) (Benth.) in relation to anatomical modifications for survival under both Pb and Ni stress. The seedlings of A. lebbeck were established and then subjected to four different concentrations, viz. 0 mM, 25 mM, 50 mM and 75 mM, of Pb and Ni for 14 days in two phases. Morphological traits such as shoot length (70.93%), fresh weight (79.27%), dry weight (83.9%), number of root hairs (65.7%), number of leaves per plant (67.4%) and number of leaflets per plant greatly reduced under Pb or Ni stress. Surprisingly, root length increased rather than decreased with the increase in Pb or Ni concentrations, along with an increase in leaflet width, leaflet length and leaflet area. Moreover, root cortical cell area, metaxylem area and phloem area decreased at 75 mM of Pb and Ni while epidermal thickness and cell area increased. Stem epidermal thickness, cell area and phloem area significantly decreased with the consistent increase in metaxylem area and cortical region thickness under both Pb and Ni stress. Leaf anatomical traits such as midrib thickness, abaxial epidermal thickness and stomatal density and adaxial epidermal thickness and stomatal area significantly increased with increasing Pb or Ni stress. Correlation analysis revealed close relations among morphological and anatomical traits (such as root length with cortical region thickness) for better plant survival under Pb or Ni stress, and a PCA-biplot further verified these correlation analyses. Cluster analyses demonstrated the associations among the morphological and anatomical traits based on different stress levels. Furthermore, we found that the longer exposure (from phase 1 to phase 2) of heavy metals stress is more dangerous for plant survival and can ultimately lead to plant death. Moreover, our results also confirmed that Ni is more harmful or dangerous to plants than Pb at high and moderate concentrations. The anatomical modifications ensured the survival of A. lebbeck in extreme heavy metals stress and therefore unlocked its potential to be used as a natural source of phytoremediation. We also recommend that the genetic potential of A. lebbeck associated with its survival under heavy metal stress be investigated.