Deoxygenation in the deep water of stratified lakes and reservoirs due to climate warming and human activities poses a threat to crucial limnetic ecosystem services. Metalimnetic oxygen minima (MOM) typically occurs during the mid to late stages of limnetic stratification. To investigate the mechanism of MOM during stably stratified periods in the Panjiakou Reservoir, northern China, four years of in-situ monitoring was conducted in parallel with longitudinal-vertical 2D modeling. The model simulated the hydrodynamic, water quality, algal, and DO processes in 2017 and 2020, and was calibrated and verified by the measurements. Three scenarios were designed to test the impact of hydrological processes and the high oxygen-consuming sedimentation zones (HOCSZ). We concluded that the stratification and the corresponding advection generated in the metalimnion are the driving forces of MOM in the reservoir, and the limnetic eutrophication-related benthic HOCSZ are the seedbeds of the metalimnetic hypoxia. This unique spatial setting driving the biogeochemical processing and MOM dynamics required a new generation of modelling, incorporating spatial inhomogeneities of sediment characteristics and a sophisticated resolution of hydrodynamics. Metalimnetic horizontal advection, hypolimnetic upwelling currents, sedimentation hot spots and the formation of high oxygen consumption zones became the major initiation processes leading to MOM. The numerical modeling not only represented the occurrence, development, and extinction of MOM but also comprehensively explained the spatial differences in the vertical morphology of MOM and its inter-annual variations. Our studies help to identify management strategies to mitigate the impacts of MOM on aquatic ecological security and drinking water quality, thus supporting the optimization of reservoir regulations.