By ship board measurement and the bottom tripod survey system，we investigate the flood damage area of fish mouth bottom structure in the south and north passage diffluence pass in the Yangtze estuary.The data analysis shows that the main reason for the south side flood damage is the scouring under the flexible mattress and the instability of concrete stone caused by the bottom vertical turbulent flow.The repair work should guarantee both the stability and the bottom protection effect of the bottom structure.