The invention provides a hypoallergenic low fishy smell fish protein oligopeptide, and an industrial preparation method and an application thereof. The preparation method comprises the following steps: 1, washing fresh fish flesh and/r fish leftover, crushing, and adding water to prepare a mixed solution; 2, carrying out heat modification on the mixed solution to prepare a denatured protein solution; 3, centrifuging the denatured protein solution, washing by using water, adding water to a precipitate obtained after the centrifuge, and grinding to prepare a slurry; 4, adjusting the pH value of the slurry to 6-9, sequentially adding neutral protease, papain and alkaline protease, carrying out enzymatic hydrolysis, and killing enzymes to prepare an enzymatic hydrolysis solution; and 5, centrifuging the above obtained second enzymatic hydrolysis liquid, carrying out membrane filtration on the obtained centrifuged supernatant to prepare the hypoallergenic low fishy smell fish protein oligopeptide. The method thoroughly eliminates the hypoallergenic property and the fishy smell of fish proteins and avoids release of bitter taste components in the fish proteins; and the mass content of peptide with the molecular weight of lower than 1000Da in the prepared oligopeptide reaches above 60%, and the oligopeptide has the advantages of high absorption rate, good mouthfeel and wide application range.