Dried flower buds of Magnolia biondii Pamp. are the main ingredient in “Xin-yi” in China, and the volatile oils of M. biondii flower buds are the principal medicinal component. Gas chromatographymass spectrometry (GC–MS) and microscopic techniques were employed to detect the volatile yields of M. biondii flowers at various growth stages. The volatile oil yields of M. biondii flowers differed significantly at different growth stages and were closely related to flower dry weight, oil cell density and degree of oil accumulation. In February 2016, flower buds had the highest dry weight, the maximum percentage of oil cells at the oil saturation stage and the highest density of oil cells, which coincided with the highest oil yield. In March 2016, flower buds had a lower dry weight, a higher percentage of oil cells at the oil-degrading stage and the lowest oil cell density, resulting in decreased oil yields. The total amounts of the major medicinal components in the M. biondii flower also showed regular changes at different growth stages. In January and February of 2016, M. biondii flowers had a higher dry weight, volatile oil yield and total content of medicinal ingredients, which was the best time for harvesting high-quality medicinal components. Our study reveals that volatile oil content and chemical composition are closely related to the growth stage of M. biondii flower buds. The results provide a scientific morphology and composition index for evaluating the medicinal value and harvesting of high-quality M. biondii medicinal herbs.