As the vessel operates in the rough open seas, a marine diesel engine simulator which engine rotation is controlled to transmit through propeller shaft is a new methodology for the self-propulsion tests to track the fuel saving in a real time. Considering the circumstance, this paper presents the real time of marine diesel engine simulator system to track the real performance of a ship through computer-simulated model. A mathematical model of marine diesel engine and the propeller are used in the simulation to estimate fuel rate, engine rotating speed, thrust and torque of the propeller thus achieve the target vessel’s speed. The input and output are real time control system of fuel saving rate and propeller rotating speed representing the marine diesel engine characteristics. The self-propulsion test simulation results in calm water [7] were compared to validate the present marine diesel engine simulator. The present simulator then was used to evaluate the fuel saving by employing a new mathematical model of turbocharged marine diesel engine and was applied to a full scale target vessel. The control system developed will be beneficial for users as to analyze different condition of vessel’s speed to obtain better characteristics and hence optimize the fuel saving rate.