In this study， ultrasonic-assisted method was used to extract total flavonoids from sea buckthorn fruits. The extraction process was optimized by the single factor test and the response surface test. The distribution and contents of four main flavonoid aglycones from sea buckthorn fruits of different maturities and different regions were determined by the optimized extraction process combined with high-performance liquid chromatography. Thereafter a comparative study of the antioxidant activity of sea buckthorn flavonoids extracts was carried out. The optimal extraction conditions were determined as follows: ethanol concentration 55%， solid-to-solvent ratio 1∶45(g/mL)， and ultrasonic power 210 W. The extraction rate of sea buckthorn A total flavonoids was up to 3.241% under the optimized conditions. The main flavonoid aglycones in sea buckthorn fruits were isorhamnetin， quercetin， kaempferol and myricetin， and the content of flavonoid aglycones varied with the maturity and region of the fruit. Total flavonoids extract from the sea buckthorn C fruits exhibited strong antioxidant activities as determined by 1，1-diphenyl-2-picrylhydrazyl (DPPH)， 2，2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)(ABTS) radical scavenging and ferric reducing antioxidant power assays. The total flavonoid aglycones content was significantly positively correlated with the DPPH radical scavenging capacity and ferric reducing power. In summary， this study can provide a scientific basis for the comprehensive utilization and development of sea buckthorn fruits.