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In recent years, the exceptional biocatalytic properties of glucose oxidase (GOx) have spurred the development of various GOx-functionalized nanocatalysts for cancer diagnosis and treatment. Carbon dots, renowned for their excellent biocompatibility and distinctive fluorescence properties, effectively incorporate GOx. Given the paramount importance of GOx's enzymatic activity in therapeutic efficacy, this study conducts a thorough exploration of the molecular-level binding dynamics between GOx and near-infrared carbon dots (NIR-CDs). Utilizing various spectrometric and molecular simulation techniques, we reveal that NIR-CDs form a ground-state complex with GOx primarily via hydrogen bonds and van der Waals forces, interacting directly with amino acid residues in GOx's active site. This binding leads to conformational change and reduces thermal stability of GOx, slightly inhibiting its enzymatic activity and demonstrating a competitive inhibition effect. In vitro experiments demonstrate that NIR-CDs attenuate the GOx's capacity to produce H 2 O 2 in HeLa cells, mitigating enzyme-induced cytotoxicity and cellular damage. This comprehensive elucidation of the intricate binding mechanisms between NIR-CDs and GOx provides critical insights for the design of NIR-CD-based nanotherapeutic platforms to augment cancer therapy. Such advancements lay the groundwork for innovative and efficacious cancer treatment strategies. • This study delves into the molecular binding mechanism between GOx and NIR-CDs. • NIR-CDs form a ground-state complex with GOx under hydrogen bonds and van der Waals forces. • NIR-CDs induces a conformational change in GOx and further reduces its thermal stability. • NIR-CDs slightly inhibit the catalytic activity of GOx via competitive inhibition mode. • NIR-CDs suppress H 2 O 2 production catalyzed by GOx, regulating cells from enzyme-induced damage. [ABSTRACT FROM AUTHOR]