In order to explore the effect of ginger juice-assisted probiotic fermentation on the flavor quality of Gastrodia elata Bl. (GE), a comparative evaluation was performed on the active constituents, sensory quality and volatile compounds of fermented GE with ginger (FGEG) and other control samples. Additionally, principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA) were used to examine the impact of ginger juice-assisted probiotic fermentation on the flavor profile of GE. Results showed that as the fermentation progressed, the content of gastrodin (GAS) increased with fluctuations, and the content of p-hydroxybenzyl alcohol (HBA) in GE significantly increased. The contents of both compounds were significantly higher in FGEG than in unfermented samples. Furthermore, ginger-assisted probiotic fermentation effectively inhibited browning in GE, preserving its color. Sensory evaluation indicated that FGEG had a unique flavor profile with odor acceptance higher than that of both fresh GE and ginger-GE mixture. Results from electronic nose and volatile compound analysis revealed that a total of 106 volatile compounds were detected during the fermentation process. Among them, the contents of aldehydes and alkenes with unpleasant odors decreased, while the content of esters with aroma increased. Hence, the fermentation improved the odor of GE to a certain extent and imparted a unique aroma to FGEG. These findings provide new insights into the development of fermented GE products, advancing the deep processing of GE.