For the construction of water conservancy project in the upstream of the Yangtze River and the human activities, the runoff and sediment discharge from the upstream to East China Sea have changed greatly. To explore the distribution characteristics of suspended sediment in Yangtze Estuary under the new upstream boundary condition, a 2-D flow-sediment numerical model including the Yangtze Estuary and the Hangzhou Bay was established. Four different runoffs, which are 4,620m³/s, 11,000m³/s, 75,900m³/s and 90,000m³/s respectively, and the correspond sediment discharges were considered. The result indicates that, with the increase of upstream runoff, the sediment intrusion from the top of the North Branch into the North Branch decreases and the suspended sediment concentration field in the South Branch changes is greater than that in the North Branch. In the same region, the sediment concentration decreases during rising tide while it increases at low tide. The change of the core position for suspended sediment field is insignificant.