Volatile compositions of different parts (stem, branch and root barks) of cortex Magnolia officinalis, cultivated in China, were investigated for the first time by GC-MS with the help of heuristic evolving latent projection (HELP). Identification of components was conducted by similarity matching to NIST mass library but also assisted by comparison of temperature-programmed retention indices (PTRIs) with the data web available. A total of 90, 82 and 76 volatile compounds in the essential oils of the three samples taken from the same batch aforementioned were qualitatively and quantitatively determined, representing 84.03, 83.68 and 83.10% of the total content, respectively. Among the constituents determined, there were 50 components coexisting. Eudesmol and its isomers were shown to be the principal compounds in the studied samples, accounting for 47.66, 36.74 and 36.31%, respectively. The three kinds of isomers (alpha-, beta- and gamma-eudesmol) in houpo volatile oils have been tentatively qualified and quantified simultaneously for the first time. By comparative analysis, significant qualitative and semi-quantitative differences and similarities were observed among the three samples. The results achieved provide a scientific evidence for further exploitation of Magnolia bark and clinical medication.