The invention relates to an engineering ship draft loading control system. The engineering ship draft loading control system comprises a central controller, a ship bow left draft sensor, a ship bow right draft sensor, a midship left draft sensor, a midship right draft sensor, a stern left draft sensor and a stern right draft sensor which are correspondingly connected with the central controller. The engineering ship draft loading control system further comprises a ship bow left draft regulator, a ship bow middle draft regulator, a ship bow right draft regulator, a stern left draft regulator, astern middle draft regulator and a stern right draft regulator which are correspondingly connected with the central controller. The central controller comprises a reliability judgment part, a fuzzy simulation analysis part, a priority control judgment part and a control instruction sending part; and according to the real-time detection data of the sensors, the adjustment precision is high, the adjustment aging is good, draft of a body of a ship is stable after adjustment, and operation and working are stable.