The aim of this work was to investigate the biochemical properties of fermented product of half-fin anchovy (HAFP; Setipinna taty) made by Natto bacillus fermentation—including molecular weight distribution, amino acid composition, solubility, foaming, and emulsifying profiles. Furthermore, the influences of thermal processing, pH alteration, and in vitro simulated gastric and intestinal digestion on the antioxidative stability of HAFP in terms of the scavenging 1,1-diphenyl-2-picrylhydrazayl (DPPH) radical were evaluated. Results showed that HAFP contained small peptides (< 1,500 Da) and free amino acids. The amounts of essential amino acids and flavor amino acids were 155.219 and 178.636 mg/g of dry HAFP, respectively. Moreover, HAFP contained high levels of antioxidative and hydrophobic amino acids. In suitable pH values, HAFP exhibited good solubility, foaming, and emulsifying properties. The antioxidative activity of HAFP on the scavenging DPPH radical increased after thermal processing. Furthermore, the DPPH radical scavenging activity of HAFP was enhanced slightly or dramatically after being treated under pH values from 3 to 6, or in vitro simulated gastric and intestinal digestion. It can be concluded that HAFP could have potential application in foods as a natural antioxidative ingredient.