Disclosed are a fish protein oligopeptide with low allergenicity and slight fishiness, and industrial preparation method and application thereof. The method comprises the following steps: 1) washing fresh fish flesh and/or fish wastes, crushing, and adding water to obtain a mixture; 2) performing thermal denaturation on the mixture to obtain a denaturized protein solution; 3) centrifuging the denaturized protein solution to obtain a precipitate, and adding water into the precipitate and grinding, to obtain a slurry; 4) adjusting the slurry to pH 6-9, and sequentially adding a neutral protease, a papain and an alkaline protease to conduct enzymolysis, and after enzyme inactivation, to obtain an enzymatic hydrolysate; 5) centrifuging the enzymatic hydrolysate, and performing membrane filtration on centrifuged supernatant, to obtain the fish protein oligopeptide with low allergenicity and slight fishiness. The method completely eliminates the allergenicity and fishiness of fish proteins, and prevents release of bitter components.