Abstarct: In the diesel electric submarines (DES), the submerged time and the capability of noiseless operation in different speeds is of special importance. To attain this purpose, it is appropriate to design the propulsion motor efficiently and select the proper supplying technique for the system using the battery banks in the various loads and speeds. To this end, in this paper a specific control structure is introduced and analyzed so as to drive a multilxayer AFPM used in the submarine propulsion system along with the capability of supplying the motor laxyers optionally in the various loads and speeds. The possibility and manner of selecting the different laxyer combinations in a multilxayer motor and supplying them is performed regarding the montage algorithm and the amount of angular shift among the different laxyers. The motor considered is a four laxyer AFPM with the rated power of tow megawatts, rotating the variable load of the propeller used in a small DES. Despite the ability of assembling and supplying a four laxyer motor with three, six, nine or twelve phases, it is demonstrated that the best selection to satisfy such an application is to supply it with a twelve-phase system. Afterwards, a novel algorithm for automatic switching of laxyers is proposed to attain the maximum efficiency in various speeds and simulate the motor transient dynamics together with the supply system in MATLAB. Finally, the matters related to the motor transient operation during switching of laxyers and the steady state characteristics in various speeds are studied.