This study aimed to isolate bacterial neuraminidase (BNA) inhibitory O-methylated quercetin derivatives from the aerial parts of S. pubescens. All the isolated compounds were identified as O-methylated quercetin (1–4), which were exhibited to be noncompetitive inhibitors against BNA, with ICsub.50 ranging from 14.0 to 84.1 μM. The responsible compounds (1–4) showed a significant correlation between BNA inhibitory effects and the number of O-methyl groups on quercetin; mono (1, ICsub.50 = 14.0 μM) > di (2 and 3, ICsub.50 = 24.3 and 25.8 μM) > tri (4, ICsub.50 = 84.1 μM). In addition, the binding affinities between BNA and inhibitors (1–4) were also examined by fluorescence quenching effect with the related constants (Ksub.SV, Ksub.A, and n). The most active inhibitor 1 possessed a Ksub.SV with 0.0252 × 10sup.5 L molsup.−1. Furthermore, the relative distribution of BNA inhibitory O-methylated quercetins (1–4) in S. pubescens extract was evaluated using LC-Q-TOF/MS analysis.