Methane is produced and emitted when organic carbon accumulates in the sediments of reservoirs. Before being released into the water body, methane can be oxidised microbially by multiple electron accepters in the sediment, and which were traditionally considered to be spatially separated from methanogens. This study provides geochemical and microbiological evidence to firstly demonstrate that methane production and oxidisation zones intersected each other in the sediment of a freshwater reservoir. Methanogens were distributed along the sediment depth profile. Hydrogenotrophic Methanomicrobiales were found to be responsible for methane production in the upper layer (< 20 cm), Hydrogenotrophic might be an active methanogenic pathway in the upper layers. Whereas Methanobacteriales and aceticlastic Methanosarcinales were responsible for methane production in the deeper layer, and aceticlastic pathway in the deeper layer. Meanwhile, the findings showed that methane was oxidised along the sediment profile. Sulfate and iron-dependent methane oxidisation dominated the surface layer and nitrite-dependent methane oxidisation prevailed in the middle layer (14–24 cm). However, the range of the sulfate zone (< 7 cm) extended deeper than the iron zone (< 5 cm). The relative abundance of Desulfobulbus and iron-oxidising bacteria (Ferritrophicum and Crenothrix) confirmed the concurrence of the sulfate and iron anaerobic-oxidation of methane (AOM) zones in the surface layer. Both of the AOM potential activity and nitrite peak indicated the active nitrite-AOM below sulfate-AOM zone. In addition to the complex crossing pattern of methane production and consumption, this work revealed a high potential of AOMs which would prevent in situ methane emissions from freshwater environments. A further investigation for the mechanism of the niche partitioning of methanogens and methane oxidizers in various types of reservoirs and the controlling factor on the distribution pattern is necessary.