Food allergies are one of the global food safety issues stated by FAO/WHO. It is a great challenges for people with food allergies to completely avoid allergens due to the diversified food processing. The development of hypoallergenic foods plays a very important role in the safety diet for people with food allergies. Technological principles of processing hypoallergenic foods were reviewed. Thermal processing technologies, such as cooking, microwave and baking, could damage allergenic conformational epitopes by heating-induced protein denaturation. Non-thermal processing technologies, such as high pressure, pulsed electric field, pulsed light, cold plasma, irradiation and ultrasound, could directly destroy allergenic epitopes through protein structure modification, polypeptide chain cleavage and generation of new chemical bonds. Other technologies, such as enzymatic hydrolysis, enzymatic cross-linking, glycosylation and microbial fermentation, could disable or hide allergen epitopes by conformational changes of protein or combining proteins and carbohydrates. In addition, the industrialized processing methods and current production status of hypoallergenic protein ingredients were also reviewed in detail. Partially and extensively hydrolyzed milk proteins of plant-based manufacture based on enzymatic hydrolysis had been achieved, and further studies should to carry out for other processes for food allergenicity reduction as well as other ingredients with hypoallergenic protein. This review hopes to provide a quick reference guide for processing hypoallergenic food at industrial scale.