As an important resource of functional food, the seeds of tree peony are rich in phenolic compounds, which are associated with antioxidant activity. However, so far there has not been systematic study on phenolic compositions and antioxidant activity of the seeds from wild tree peony species. The aim of this study was to determine the phenolic content, antioxidant compounds and antioxidant activity of seeds from nine tree peony species native to China. Among the seed samples, Paeonia rockii had the highest total flavonoid content, strongest DPPH and ABTS radical scavenging activities, and strongest cupric reducing capacity; P. decomposita subsp. rotundiloba had the highest total phenolic and flavanol contents, as well as the strongest hydroxyl radical scavenging activity. Sixteen individual phenolic compounds were quantitatively measured, with (+)-catechin being the most abundant component. The content of the phenolic compounds luteolin, paeonol, and the total flavonoid content were significantly correlated with four antioxidant activities. Hierarchical cluster analysis showed that P. rockii and P. decomposita subsp. rotundiloba could be clustered in a group having a high phenolic content and strong antioxidant activity. These results suggest P. rockii and P. decomposita subsp. rotundiloba are the most promising candidates as useful sources of natural antioxidants.