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This study aimed to isolate bacterial neuraminidase (BNA) inhibitory O-methylated quercetin derivatives from the aerial parts of <i>S. pubescens</i>. All the isolated compounds were identified as O-methylated quercetin (<b>1</b>–<b>4</b>), which were exhibited to be noncompetitive inhibitors against BNA, with IC₅₀ ranging from 14.0 to 84.1 μM. The responsible compounds (<b>1</b>–<b>4</b>) showed a significant correlation between BNA inhibitory effects and the number of O-methyl groups on quercetin; mono (<b>1</b>, IC₅₀ = 14.0 μM) > di (<b>2</b> and <b>3</b>, IC₅₀ = 24.3 and 25.8 μM) > tri (<b>4</b>, IC₅₀ = 84.1 μM). In addition, the binding affinities between BNA and inhibitors (<b>1</b>–<b>4</b>) were also examined by fluorescence quenching effect with the related constants (<i>K</i>_SV, <i>K</i>_A, and <i>n</i>). The most active inhibitor <b>1</b> possessed a <i>K</i>_SV with 0.0252 × 10⁵ L mol⁻¹. Furthermore, the relative distribution of BNA inhibitory O-methylated quercetins (<b>1</b>–<b>4</b>) in <i>S. pubescens</i> extract was evaluated using LC-Q-TOF/MS analysis.