Using technical means of 2-dimensional tidal current and sediment mathematical model , with monographic study on choosing flume of 12.5 m deepwater channel phase Ⅱ project of Kou’an straight reach along Yangtze River downstream Nanjing, selecting typical calculation conditions of water and sediment, the contrast calculation and analysis are conducted of tidal current and sediment movement before and after the choice of flume , along with back silting quantity calculation within the position dredging of the design channel, providing a scientific basis for the scheme determination of choosing flume for Manyusha shoal reach. The calculation of mathematical model indicates that: plan 1 has effect on beach protection and increasing the flow dynamics of the channel shallow section, with less influence on surrounding waters. Considering the maintainability of the channel, adaptability of the traffic organization and adaptability of the coastal ports at the same time, plan 1 is recommended as scheme for choice of flume (unidirectional channel in left and right branch) of 12.5 m deepwater waterway in Kou’an Straight reach Manyusha shoal reach, while in the scheme a slight adjustment to the left bank of the middle route in the left flume is suggested, adapting to the change trend in the deep flume.