In the first phase project of 12.5 m deepwater channel of the Yangtze River downstream Nanjing, under the worst working condition for the mattress placing ship, the water depth is 35 m, flow velocity is 2 m/s, and angle of current is 20 degrees. If we use the conventional placing operation method, the anchor cable stress often appears uneven situation. When the anchor cable stress exceeds the set value, the placing ship will lose mooring control. It is the main factor affecting safety. If it’s not effectively controlled, it may cause works accident. Therefore, in combination with the relevant information at home and abroad and the first phase project field operation of 12.5 m deepwater channel of the Yangtze River downstream Nanjing, this paper carries out the calculation analysis using the probability method and ANSYS finite element software, analyzes the anchor cable stress system on the placing ship in big flow velocity, deep depth and shifting current conditions, and puts forward the optimization of anchor system and servo anchor system control method. Through verification by engineering application, optimization of anchor system in combination with follow-up method is reasonable, can effectively control the difficult problem of losing mooring control in harsh conditions, and provides the referential experience for solving similar phenomenon.