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<i>Magnolia champaca</i> (L.) Baill. ex Pierre of family Magnoliaceae, is a perennial tree with aromatic, ethnobotanical, and medicinal uses. The <i>M. champaca</i> leaf is reported to have a myriad of therapeutic activities, however, there are limited reports available on the chemical composition of the leaf essential oil of <i>M. champaca</i>. The present study explored the variation in the yield and chemical composition of leaf essential oil isolated from 52 accessions of <i>M. champaca</i>. Through hydrodistillation, essential oil yield was obtained, varied in the range of 0.06 ± 0.003% and 0.31 ± 0.015% (<i>v</i>/<i>w</i>) on a fresh weight basis. GC-MS analysis identified a total of 65 phytoconstituents accounting for 90.23 to 98.90% of the total oil. Sesquiterpene hydrocarbons (52.83 to 65.63%) constituted the major fraction followed by sesquiterpene alcohols (14.71 to 22.45%). The essential oils were found to be rich in β-elemene (6.64 to 38.80%), γ-muurolene (4.63 to 22.50%), and β-caryophyllene (1.10 to 20.74%). Chemometrics analyses such as PCA, PLS-DA, sPLS-DA, and cluster analyses such as hierarchical clustering, i.e., dendrogram and partitional clustering, i.e., K-means classified the essential oils of <i>M. champaca</i> populations into three different chemotypes: chemotype I (β-elemene), chemotype II (γ-muurolene) and chemotype III (β-caryophyllene). The chemical polymorphism analyzed in the studied populations would facilitate the selection of chemotypes with specific compounds. The chemotypes identified in the <i>M. champaca</i> populations could be developed as promising bio-resources for conservation and pharmaceutical application and further improvement of the taxa.