The change in volatile compound composition of three wild chrysanthemum species (Chrysanthemum boreale, C. indicum, and C. indicum var. albescens) was identified and analyzed according to four flowering stages using HS-SPME-GC-MS (headspace solid-phase microextraction coupled to gas chromatography–mass spectrometry). The top five compounds of each flowering stage were selected because those main compounds accounted for 43.25%, 44.14%, and 54.20% of the total relative content of volatile compounds from C. boreale, C. indicum, and C. indicum var. albescens, respectively. Nine compounds (1S-α-pinene, α-thujone, chrysanthenone, umbellulone, thymol, caryophyllene, germacrene D, α-zingiberene, and α-patchoulene) in C. boreale were ranked in the top five compounds through the whole flowering stages. In C. indicum, camphene, eucalyptol, camphor, umbellulone, bornyl acetate, caryophyllene, β-farnesene, germacrene D, and α-zingiberene were ranked in the top five compounds. However, only five compounds (camphor, bornyl acetate, β-farnesene, germacrene D, and α-zingiberene) were ranked in C. indicum var. albescens showing a more stable composition rather than C. boreale and C. indicum. Flowerheads of three wild Chrysanthemums showed a different profile of volatile compounds according to different flowering stages, varying compositions, and relative content in the top five volatile compounds. This study illustrates how main volatile compounds in wild chrysanthemums change dynamically during the flowering regarding compositions and their relative contents, suggesting that it should provide a useful index for harvesting or blending certain target compounds from wild chrysanthemums.