To clarify the aromatic compounds of sea buckthorn and their formation pathways, the key aroma compounds in Hippophae rhamnoides subsp. sinensis were determined first. There were 21 compounds identified as the key aroma components (e.g. ethyl isovalerate, ethyl caproate, ethyl octanoate, 1-hexanol, 1-nonanol, phenylethyl alcohol, nonanal, 6-methyl-5-heptene-2-one) of sea buckthorn, which were mainly composed of esters and alcohols. There were obvious differences in the composition of compounds among Hippophae rhamnoides subsp. sinensis (SI, SS) and Hippophae rhamnoides subsp. thibetana (TS). Esters were the main volatiles of Hippophae rhamnoides subsp. sinensis (SI, SS), while alcohols were the main volatiles of Hippophae rhamnoides subsp. thibetana (TS), which resulted in a lack of overall aromas in TS and a strong fruity and winy odor in SI and SS. The aroma of sea buckthorn could be reproduced well by analyzing key aroma components. Additionally, oleic acid, linoleic acid, leucine, phenylalanine, lycopene, and other compounds generated key aroma compounds by fatty acid oxidation pathway, amino acid degradation pathway, mevalonic acid pathway, methylerythritol phosphate pathway, carotenoid degradation pathway. Therefore, the key aroma compounds in sea buckthorn berries and their metabolic pathways were studied in the paper, which provided the research basis for genetic breeding and fine processing of sea buckthorn.