Sea buckthorn (Hippophaë rhamnoides L.), as one of the Elaeagnaceae family, has the significant function of anti-tumor, anti-inflammation, anti-oxidation, and other physiological activities. High hydrostatic pressure (HHP) extraction has the advantages of being easy and efficient, while maintaining biological activity. In this study, sea buckthorn flavonoid (SBF) was extracted with HHP and purified sea buckthorn flavonoid (PSBF) was isolated by AB-8 macroporous resin column. HPLC analysis was used to quantified them. In addition, the effect of anti-allergy in RBL-2H3 cells by SBF, PSBF, and their flavonoid compounds was evaluated. The results demonstrate the conditions for obtaining the maximum flavonoid amount of SBF: 415 MPa for 10 min, 72% ethanol concentration, and a liquid to solid ratio of 40 mL/g, which increased the purity from 1.46% to 13.26%. Both SBF and PSBF included rutin, quercitrin, quercetin, isorhamnetin, and kaempferol. In addition, quercitrin, kaempferol, and SBF could regulate Th1/Th2 cytokine balance. Moreover, extracellular Ca2+ influx was reduced by quercitrin and PSBF. Furthermore, rutin, quercetin, iso-rhamnetin, and SBF could also inhibit P-p38 and P-JNK expression, thereby suppressing the phosphorylation of the MAPK signaling pathways. Overall, SBF is effective for relieving food allergy and might be a promising anti-allergic therapeutic agent.