Inland waters are considered to be a significant source of methane (CH₄) emissions, accounting for 25% of total global CH₄ emissions. This study was conducted to analyze the changing characteristics of CH₄ fluxes at the water-gas interface and the influence of methane-functional bacterial communities on methane emissions in the Inner Mongolia section of the Yellow River. Samples were collected from March to November 2023, and the static box-gas chromatography was used to explore the spatio-temporal characteristics of CH₄ fluxes at the water-gas interface and analyse its main influencing factors. Additionally, high-throughput sequencing techniques of the 16S rRNA gene were used to investigate the relationship between methane-functional bacterial communities and methane emissions. It was found that the Inner Mongolia section of the Yellow River generally behaved as a source of atmospheric CH₄ emissions during the study period, and its CH₄ emission fluxes were (5.92±4.54) mg m^-2 d^-1, (13.42±18.83) mg m^-2 d^-1, and (1.40±3.81) mg m^-2 d^-1 in spring, summer, and autumn, respectively, with significant seasonal variations and significant spatial variability of the CH₄ emission fluxes at different sampling points. CH₄ gas fluxes were influenced by various environmental factors, and were significantly negatively correlated with dissolved oxygen (DO) (P < 0.05), and significantly positively correlated with dissolved organic carbon (DOC) and ammonium nitrogen (NH₄⁺-N) (P < 0.01 and P=0.05). The study area showed Methanosarcina and Methanobacterium as the dominant groups of methanogenic bacteria, while Methylocystis and Methylobacter were the dominant groups of methane-oxidizing bacteria. There were significant differences in the diversity and abundance of methane-functional bacteria in the different samples, with the environmental factor that had the greatest effect on methanogenic bacteria being total carbon (TC)(r=0.8792) and the environmental factor that had the greatest effect on methane-oxidizing bacteria being NH₄⁺-N (r=0.7190). Among methanogenic bacterial communities, Methanobacterium and the unclassified genus unclassified_k_ norank_d_Archaea had the greatest impact on CH₄ emissions, and this group of bacteria promoted methane emissions. Among the methane-oxidizing bacterial communities, the unidentified methane-oxidizing bacterium norank_d_Bacteria had the greatest impact on CH₄ oxidation, and this group of bacteria promoted methane oxidation and thus reduced methane emissions at the water-gas interface. This study can provide data support for the estimation of greenhouse gases (GHG) emissions from rivers in China as well as emission mechanisms.