Fruits are rich in vitamins, polyphenols and other antioxidants, which can delay aging and promote human health. However, fruit allergy induced food safety issues are increasing recently. The common fruit allergens and cross-reactivity allergy, as well as the principles and research progress of mitigation technology in fruit allergy were summarized. There were mainly seven types of common fruit allergens including thaumatin like protein (TLP), Bet v 1 homologous protein, lipid transfer protein, profilin, chitinase, cysteine protease and β-1,3-glucanase. Cross-reactivity allergy was one of the main factors causing fruit allergies, when multiple allergens contained similar structural sequences or determinants. Among them, Bet v 1 in pollen was most likely to trigger cross-reactivity allergy with common fruits. Physical processing technologies including high temperature, high pressure, pulsed electric field, ultrasound, and irradiation could directly destroy the structure of fruit allergens by breaking and rearranging the disulfide bonds, strengthening or weakening the hydrogen bonds, as well as breaking or cross-linking peptide chains. Chemical mitigation techniques such as lye or enzyme treatment could degrade epitopes in fruit allergens by disrupting their protein structures. At present, very limited studies were performed on the mitigation technologies of fruit allergens, and their effects of reducing the fruit allergenicity hardly reached ideal level. In the future, the combination of multiple technologies such as molecular dynamics simulation and novel food processing technologies could be used to precisely target and control fruit allergenicity. Innovative technologies including biological breeding and genome editing can cultivate new varieties of desensitized fruits, which fundamentally solve the challenges caused by fruit allergy, providing a scientific basis for the development and industrial application of hypoallergenic or desensitized fruit products.