Chrysanthemum boreal, C. indicum, and C. indicum var. albescens are well-known wild Chrysanthemum species used for traditional medicine in Korea. In this study, volatile compounds from three wild Chrysanthemums were identified according to four different flowering stages and analyzed using HS-SPME-GC-MS to determine the temporal variation of the volatiles. As a result, 132, 151, and 142 peaks were identified from C. boreale, C. indicum, and C. indicum var. albescens, respectively. Furthermore, 70 out of 132 peaks were identified in C. boreale with a matching ratio of >90% from library search. In addition, 85/151 and 76/142 peaks were identified from C. indicum and C. indicum var. albescens. Forty-nine volatile compounds were found commonly in all three wild Chrysanthemums through all four different flowering stages. However, six, seven, and five unique compounds were detected only in C. boreale, C. indicum, and C. indicum var. albescens, respectively. One hundred volatile compounds were selected for multivariate analysis considering volatile compounds overlapped with each other. The one-way ANOVA (p < 0.05) detected significant differences from 77 out of 100 volatile compounds. In addition, PLS-DA showed the different profiles of volatile compounds according to four different flowering stages in each wild Chrysanthemum. PC1 of each Chrysanthemum accounted for 45.8 56.9, and 11.9% in C. boreale, C. indicum, and C. indicum var. albescens, respectively. PC1 of C. boreale and C. indicum clearly separated the BF stage and the other three stages. Conversely, PC1 of C . indicum var. albescens showed a difference in the composition of volatile compounds between the BF/BO and HO/FO stages. In addition, the different profiles of volatile compounds could be visualized using a heatmap from three wild Chrysanthemums according to four different flowering stages. This study will help improve particular volatile compounds in three wild Chrysanthemums both in quality and quantity.