This study aims to make the function of the propulsion system on ship flexible at various working conditions on sea, and it concentrates on the abnormal conditions that form a hard challenge for the ship. We dealt in this paper some abnormal working cases; include sailing in shallow waters, storm condition and fouling on ship hull. At these three cases there is a rise in stress on engine parts, higher fuel consumption, decrease in the speed of the ship and other problems. To solve these problems we developed a program on C# language, that simulate the elements of propulsion system on ship and coordinates between the engine and the propeller through varying some parameters to ensure sailing of ship at suitable speed, at optimal fuel consumption for the engine, and to keep the propulsion elements at good state.