Safety risk during the construction of a Large Scale Engineering (LSE) project can be avoided through safety education, following a correct procedure and using an engineering method. In order to ensure that LSE works in a safe state, some parameters need to be restricted to a certain range. Besides, in order to apply the former control for the predictive values, a Model Predictive Control (MPC) theory is suggested to be used for safety risk controlling. We share a MPC work flow and detail calculation steps of the rolling optimization, feedback correlation and constraint control, and a mean time gradient decent method is used during the optimization calculation iteration steps. At the end, regarding the resource allocation issue in the ship-lift engineering construction area of “Three Gorges” we verify how MPC works; and the numeric results show MPC’s efficiency. We can see that MPC might have important future in safety risk management of LSE, because as long as the model can be predictive, regardless of an accurate mathematical model of the system, MPC can control a dynamic and uncertain system very well, which is also a characteristic of the safety risk of LSE.