Atraphaxis virgata and Atraphaxis pyrifolia are xerophytic species of the Polygonaceae family that remain insufficiently characterized from pharmacognostic, phytochemical, and toxicological perspectives. This study provides an integrated evaluation of both species through anatomical authentication, sequential extraction of CO₂-extracted residual biomass, GC–MS and LC–MS metabolite profiling, and acute oral toxicity assessment. Anatomical analysis revealed shared xeromorphic traits, including cuticular protection, dorsiventral mesophyll organization, structured vascular bundles, and calcium oxalate druses. It also identified species-specific differences in leaf thickness, mesophyll arrangement, vascular architecture, and druse morphology. GC–MS analysis showed distinct chemical profiles: A. virgata displayed a concentrated profile dominated by acetophenone- and benzofuran-related constituents, whereas A. pyrifolia showed a broader spectrum of carbohydrate-derived, phenolic-related, and oxygenated constituents. LC–MS analysis supported the tentative annotation of diverse polyphenolic classes, including flavonoids, phenolic acids, coumarins, and phenylpropanoid derivatives. Acute oral toxicity testing showed no mortality at doses up to 2000 mg/kg, supporting a low acute oral toxicity classification under the tested conditions. However, histological examination revealed mild to moderate dose-dependent alterations in liver and kidney tissues at higher doses. The novelty of this work lies in linking diagnostic anatomical traits, species-specific metabolite patterns, residual biomass valorization, and preliminary safety evidence within a single comparative framework. These findings provide a basis for pharmacognostic authentication, phytochemical standardization, and future bioactivity-guided evaluation of Atraphaxis species.