Submersible motor is of lathy subsection structure of stator and rotor and the leakage reactance in subsection impact on motor performance. Three-dimensional finite element mathematic model of submersible motor magnetic isolated segment used to calculate leakage reactance corresponding to the leakage magnetic field in it is established in this paper. Simulation prototype is designed. The accuracy and feasibility of the method described here is directly verified by example comparison. This leakage reactance has bigger influence to performance parameter of the motor and must be taken into account in the design of submersible motor for the future.