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Gastrodia elata(G. elata) is a traditional Chinese herbal medicine. In recent years, G. elatahas been widely used in food and pharmaceutical industries because of its excellent health benefits. However, the stability and bioactivity of phenolic compounds from G. elataafter in vitrogastrointestinal digestion remain unknown. In this study, the aqueous extract of G. elatarhizomes was used to simulate gastrointestinal digestion and colonic fermentation in vitro. This study aimed to evaluate the bioaccessibility during the simulation of gastrointestinal and colonic fermentation and to clarify the effects of different digestion stages on the anti-oxidant and enzyme inhibitory activities and intestinal health of samples in vitro. The results indicated that the total polyphenol and flavonoid contents after colonic fermentation for 72 h were 5.48- and 3.24- fold higher than those without digestion, respectively. Except for gastrodigenin and ferulic acid, the contents and bioaccessibility of the other phenols after fermentation were higher than those in the small-intestine stage. Antioxidant activity was positively correlated with the total polyphenol content. The inhibitory activities of pancrelipase and cholinesterase were enhanced by gastric digestion and colonic fermentation. The sample promoted the production of Lactobacillusand decreased the abundance of pathogenic bacteria. Moreover, the content of short-chain fatty acids also exhibited an upward trend. Therefore, G. elatahas the potential to develop into a health food with anti-oxidant, anti-obesity, and intestinal health functions.