The accurate estimation of the zigzag leakage flux losses (ZZLFL) caused by the slot harmonics and their interactions, which occupy a high proportion of stray losses, are of great significance in the efficiency calculation as well as the optimization design for the wet submersible induction machine (WSIM). In this paper, a two-dimensional finite element method (FEM) is presented to separate ZZLFL into the iron losses and the eddy-current losses. The air-gap magnetic flux density is decomposed by the two-dimensional fast Fourier transform at a sampling frequency of 5000 Hz. The hybrid excited virtual permanent magnet harmonic machine model is applied to reconstruct the air-gap magnetic field and excite the stator and rotor separately. Each node harmonic iron losses are acquired through the modified Bertotti iron losses model with the consideration of high-frequency power losses as a function of the magnetic flux density. The zigzag flux losses provided by different harmonics are obtained by subtracting the hybrid excitation losses. According to the different proportions of harmonic losses among zigzag flux losses, novel WSIM models are proposed in the paper to decrease zigzag flux losses and increase the efficiency. Adopting the same computation process, the novel models with different structures are explored and verified to improve the zigzag flux losses and power density.