To clarify the water ecological restoration mechanism of low water level operation in urban rivers, indoor simulation experiments were conducted, including vertical monitoring of water, physicochemical indicators of sediment, quantitative monitoring of microbial functional genes, and measurement of microbial activity. The change characteristics of environmental factors at the mud-water interface and dissolved oxygen in sediment were analyzed, the change characteristics in the main pollutants and functional microorganisms in sediment were studied, and the synergistic coupling process of upper nitrification and lower denitrification in polluted sediment under low water level operation were revealed.The results show that low water level operation can change the “source sink” property of sediment, and the “source” at high water level can be transformed into a “sink” at low water level, thereby achieving an improvement in water quality.With the restoration of polluted sediment, a multi nutrient level complete aquatic ecosystem consisting of benthic animals, submerged plants, emergent plants, insects, and birds can gradually be formed. The treatment of polluted sediment is the key to ecological restoration, and urban rivers can achieve self-restoration of sediment and ecosystem construction under low water level operation mode. Keywords: urban rivers; low water level operation; sediment pollution; ecological restoration