The invention discloses a system optimization method and device of ship operation energy efficiency. The method comprises the steps of data acquisition, mathematical model establishment, analysis and calculation, output and execution; namely, acquiring speed over water and speed over ground of the ship, real-time rotating speed and instant oil consumption of ship main engine; when the ship is in much deeper water, establishing a mathematical model between the real-time rotating speed of the ship main engine and the ship speed over water and a mathematical model between the real-time rotating speed of the ship main engine and the instant oil consumption of the ship main engine; analyzing and calculating the mathematical models under different water flow velocities and different main engine rotating speeds to obtain the ship kilometer oil consumption valves of the ship corresponding to different conditions; displaying the ship kilometer oil consumption value and the corresponding main engine rotating speed to guide the operation. The method also includes a ship technical state judging and navigation operating optimizing method. The device comprises a central processer and a memory thereof, a data acquisition equipment, man-machine conversation equipment, output equipment, a power supply unit and the like.