(1) Background: Propolis has attracted attention in recent years due to its important pharmacological effects. The present study aimed to investigate the botanical origins of 39 propolis samples and evaluate their antioxidant activities; (2) Methods: A HPLC-PDA system was used to analyze the phenolic compositions of propolis and poplar bud resin samples. The antioxidant activities of propolis samples were evaluated by oxygen radical absorption capacity (ORAC) and superoxide anion free radical scavenging capacity assay; (3) Results: Our study shows that 17 propolis samples were characterized by five predominant flavonoids, including 5-methoxy pinobanksin, pinobanksin, pinocembrin, pinobanksin-3-acetate, and chrysin, while 22 propolis samples were characterized by four flavonoids (pinobanksin, pinocembrin, pinobanksin-3-acetate, and chrysin). The average contents of characteristic flavonoids reached up to over 70% and 65% of total phenolics, respectively. Furthermore, the botanical origins of the two types of propolis samples were identified asPopulus×euramericanacv. ‘Neva’ andPopulus Simonii×P.nigra, respectively; (4) Conclusions: Most notably, our results reveal that these propolis samples presented excellent antioxidant activities due to their high contents of flavonoid. These flavonoid-rich propolis samples can thus be used to develop low-allergen and high-antioxidant nutraceuticals.