The changes in quality properties and nutritional components for two mugworts, namely, Artemisia capillaris Thumberg Artemisiae asiaticae Nakai fermented by Bacillus strains were characterized followed by rapid pattern analysis of volatile flavor compounds through the SAW-based electronic nose sensor in the GC system. After fermentation, the pH has remarkably decreased from 6.0∼6.4 to 4.6∼5.1 and there has been a slight change in the total soluble solids. The L (lightness) and b (yellowness) values in the Hunter's color system significantly decreased, whilst the a (redness) value increased via fermentation. The HPLC analysis demonstrated that the total amino acids increased in quantity and the essential amino acids were higher in the A. asiaticae Nakai than in the A. capillaris Thumberg, specially with high contents of glutamic and aspartic acid. After fermentation, the monounsaturated fatty acid increased in the A. asiaticae Nakai and the polyunsaturated fatty acids increased in the A. capillaris Thumberg. While the total polyphenol contents have not been affected by fermentation, the total sugar contents have dramatically decreased. Scopoletin, which is one of the most important index components in mugworts, was highly abundant in the A. capillaris Thumberg; however, it was not detected in the A. asiaticae Nakai. Small pieces of plant tissue in the surface microstructure were found in the fermented mugworts through the use of the scanning electron microscope (SEM). Volatile flavor compounds via electronic nose showed that the intensity of several peaks has increased and additional seven flavor peaks have been produced after fermentation. The VaporPrintTM images demonstrated a notable difference in flavors between the A. asiaticae Nakai and A. capillaris Thumberg, and the fermentation enabled the mugworts to produce subtle differences in flavor.