This study aimed to evaluate the quality characteristics of Gastrodia elata Blume fermented by lactic acid bacteria after saccharifying by 3 methods including enzyme, malt, and rice-nuruk. The lactic acid bacteria (LAB), Pediococcus inopinatus BK-3, isolated from kimchi could reduce the unpleasant taste and odor of Gastrodia elata Blume. The total acidity value of Gastrodia elata fermented by LAB on the malt and rice-nuruk extract solution for 3 days was 2.23% and 2.33%, respectively. After saccharification by malt and rice-nuruk extract solution for 3 days, the viable cell number of fermented Gastrodia elata was 9.14 log cfu/mL and 9.27 log cfu/mL, respectively. The total acidity values were increased above 3.35% by malt and rice-nuruk extract solution for 8 days. Thus, the viable cell number was the highest by malt and rice-nuruk extract solution fermentation for 3 days. The amino acid content of Gastrodia elata fermented by LAB after saccharification by malt extract solution was higher than that of other saccharifying methods. The free sugar content and p-hydroxybenzyl derivatives induced by the enzyme method were higher than those of other saccharifying methods. The overall acceptability was the highest at 4.2 point in Gastrodia elata fermented by malt extract solution.