Due to the high sediment content in the operation of the reservoirs in sediment-laden rivers, the effective reservoir storage capacity is often occupied by serious sediment deposition, which leads to the reduction of the service life of the reservoir and the damage to the comprehensive benefit of the reservoir. In order to ensure the sufficient and long-term operation of the sediment laden river reservoirs, three sediment deposition patterns for sediment laden river reservoirs were revealed based on the changes in sediment erosion and deposition during the sediment retention period and normal operation period of the reservoirs, including high beach with deep channel, middle channel and high channel. A coupling design method between the sediment deposition patterns and the storage capacity distribution in the sediment-laden river reservoirs was proposed. The storage capacity distribution model of deep channel for sediment regulation, middle channel for profit promotion, and high channel for flood regulation was established. A new design method of flood control high water level, check flood level and migration level is developed based on the siltation form of high beach and high channel.