Procyanidin is an important polyphenol for its health-promoting properties, however, the study of procyanidin in sea buckthorn was limited. In this paper, sea buckthorn procyanidin (SBP) was obtained through a green isolation and enrichment technique with an extraction rate and purity of 9.1% and 91.5%. The structure of SBP was analyzed using Ultraviolet-visible spectroscopy (UV-vis), Fourier-transform infrared spectroscopy (FT-IR), and liquid chromatography-mass spectrometry (LC-MS/MS). The results show that SBP is an oligomeric procyanidin, mainly composed of (-)-epicatechin gallate, procyanidin B, (+)-gallocatechin-(+)-catechin, and (+)-gallocatechin dimer. SBP showed superior scavenging capacity on free radicals. Furthermore, the cleaning rate of the ABTS radical was 4.8 times higher than vitamin C at the same concentration. Moreover, SBP combined with vitamin C presented potent synergistic antioxidants with combined index values below 0.3 with concentration rates from 5:5 to 2:8. SBP also provided significant protection against oxidative stress caused by hydrogen peroxide (H2O2) on RAW264.7 cells. These findings prove the potential of SBP as a natural antioxidant in food additives and support the in-depth development of sea buckthorn resources.