The prevalence of hypoxia in surface sediment inhibits the growth of aerobic denitrifiers in natural waters. A novel oxygen micro/nanobubble-loaded microporous biochar (OMB) was developed to activate indigenous aerobic denitrifiers in this study. The results indicate a thin-layer OMB capping mitigates hypoxia effectively. Following a 30-day microcosm-based incubation, a 60 % decrease in total nitrogen concentration was observed, and the oxygen penetration depth in the sediment was increased from <4.0 mm to 38.4 mm. High-throughput sequencing revealed the stimulation of indigenous mixotrophic aerobic denitrifiers, including autotrophic de-nitrifiers such as Hydrogenophaga and Thiobacillus, heterotrophic denitrifiers like Limnobacter and unclassi-fied_f_Methylophilaceae, and heterotrophic nitrification aerobic denitrification bacteria, including Shinella and Acidovorax, with total relative abundance reaching up to 38.1 %. Further analysis showed OMB enhanced the overall collaborative relationships among microorganisms and promoted the expression of nitrification-and denitrification-related genes. This study introduces an innovative strategy for stimulating indigenous aerobic denitrifiers in aquatic ecosystems.