Due to the influence of the Three Gorges dam, the water stage of the hydraulic wharf engineering of Nanjing port Longtan area was unusual and thus the smooth completion of project during the scheduled period can’t be guaranteed. So, unusual measures shall be taken. This paper introduces the reasonable organization of construction under abnormal stage. By increasing the construction labor and turnover materials and machines for the underwater buildings before the next tide flood, we finished the construction of wharf’s underwater buildings.