Local scour in Baimaosha channel project of the first phase of the Yangtze River deep water channel project from Nanjing areis studied by local normal model. The results show that: 1) S1 groyne, S2 groyne, S3 groyne and the head of south polder dike, etc. are positions prone to appear significant local scour in Baimaosha channel project, and thus need to focus on protection; 2) Optimization scheme is not only effective to prevent local scour, but also scientific and rational in layout design of flexible mattress, thus can meet the needs of engineering safety and conservation investment.