To investigate the changes in the release and functional activity of total flavonoids and total polyphenols of Camellia fascicularis during the digestion, the total flavonoid and total polyphenol contents, as well as free radical scavenging ability, iron ion reducing ability, and lipid peroxidation inhibitory ability of the C. fascicularis digestive fluid were determined using an in vitro simulated gastrointestinal digestion model, and the analysis of their correlation was performed. The results showed that during simulated gastric digestion, the total flavonoid and total polyphenol contents of C. fascicularis were higher than thoseduring oral digestion, with the highest values reaching 229.99 and 327.65 μg/mL, respectively. After the intestinal digestion, the total flavonoid and total polyphenol contents were both low, ranging from 38.56 to 78.88 μg/mL, and 30.04 to 65.52 μg/mL, respectively. In the functional activity assay, DPPH and ABTS+• scavenging abilities and iron ion reducing ability were significantly higher in the gastric digestion phase than in the oral digestion, while the lipid peroxidation inhibitory ability fluctuated with the progress of digestion. After the intestinal digestion, DPPH and ABTS+•scavenging abilities and iron ion reducing ability decreased sharply after the intestinal digestion, which were lower than those during gastric digestion, whilst the lipid peroxidation inhibitory ability tended to be stable or increased gradually. The correlation analysis and principal component analysis revealed that there was certain correlations between the indicators. In summary, C. fascicularis is a better source of active substances. This study can provide a certain experimental basis and new ideas for exploring the changes of active substances and their working mechanisms during human digestion of C. fascicularis.