Abstract: Deep liquid-state fermentation is considered an effective method for enhancing the phytochemical properties and metabolism of traditional Chinese medicinal plants. This study optimized the enzymatic hydrolysis process of Gastrodia elata using response surface methodology, selected the most suitable Lactobacillus plantarum strains for fermentation of Gastrodia enzymatic hydrolyzate (GEH), investigated the optimal fermentation conditions through single-factor experiments, and analyzed the changes in bioactive components before and after fermentation. The study investigated the fermentation of GEH by Lactobacillus plantarum strains LZU-J-TSL6 and LZU-LJY-1Q1 in a 1:1 ratio, and analyzed its physicochemical properties, antioxidant activity, and metabolomic characteristics. The results indicated that under the conditions of liquid-to-material ratio of 30:1 (mL/g), enzymolysis time of 2 h, enzymolysis temperature of 67 °C, and enzyme amount of 0.5%, the highest levels of gastrodin and hydroxybenzyl alcohol were achieved. Furthermore, after 18 h of fermentation at 37 °C with a 3% inoculation rate (10⁸ CFU/mL), viable counts in the fermented Gastrodia enzymatic hydrolyzate (FGEH) were the highest. In comparison to GEH, the titratable acidity, total polysaccharide content, and total phenolic acid content in FGEH increased by 419.35%, 12.72%, and 32.61%. Additionally, the scavenging activities of ABTS⁺, DPPH, and OH free radicals improved by 24.27%, 38.96%, and 17.78%. Full-target metabolomic analysis revealed that, compared to GEH, 56 metabolites were significantly upregulated in FGEH, including N-(1-deoxy-1-fructosyl)leucine and gentiotriose, while 35 metabolites were significantly downregulated, such as gastrodin and L-aspartic acid. FGEH was found to primarily affect KEGG pathways related to ABC transporters and galactose metabolism. This study provides a theoretical foundation for the development of traditional Chinese medicine derived from Lactobacillus plantarum fermented medicinal and food homologs.