Torreya grandis is an important economic forestry product in China, whose seeds are often consumed as edible nuts, or used as raw materials for oil processing. To date, as an important by-product of Torreya grandis, comprehensive studies regarding the Torreya grandis seed coat phenolic composition are lacking, which greatly limits its in-depth use. Therefore, in the present study, the Torreya grandis seed coat was extracted by acid aqueous ethanol (TE), and NMR and UHPLC-MS were used to identify the major phenolics. Together with the already known phenolics including protocatechuic acid, catechin, epigallocatechin gallate, and epicatechin gallate, the unreported new compound 2-hydroxy-2-(4-hydroxyphenylethyl) malonic acid was discovered. The results of the antioxidant properties showed that both TE and 2-hydroxy-2-(4-hydroxyphenylethyl) malonic acid exhibited strong ABTS, DPPH, and hydroxyl radical-scavenging activity, and significantly improved the O/W emulsion’s oxidation stability. These results indicate that the TE and 2-hydroxy-2-(4-hydroxyphenylethyl) malonic acid could possibly be used in the future to manufacture functional foods or bioactive ingredients. Moreover, further studies are also needed to evaluate the biological activity of TE and 2-hydroxy-2-(4-hydroxyphenylethyl) malonic acid to increase the added value of Torreya grandis by-products.