Antique Lotus (Nelumbo) is a perennial aquatic plant with unique historical significance and cultural value, whereas its potential economic value hasn’t been fully explored. The present study showed that lotus seedpods had significantly higher antioxidant capacity than other parts by FRAP, ABTS, and ORAC assays and analyzed the proanthocyanidins and flavonols in the seedpods of Antique Lotus. Polyphenols contributed to great antioxidant activity and 51 polyphenols were identified by UPLC-TQ-MS analysis. In which, 27 compounds were identified from lotus seedpods for the first time, including 20 trimers, 5 dimers and 2 tetramers of proanthocyanidin. Total proanthocyanidins explained 70%–90% of the different antioxidant activities and the content of proanthocyanidin trimers showed the strongest correlations with the antioxidant activities. This study provided a fundamental reference for the research of polyphenols in lotus and found that Antique Lotus seedpod extracts have the promising prospects of additives used in feed and food processing.