The physics of aluminum electrolysis process involves many spatial scales, generating a wide variety of bubbles of different sizes in the magnetohydrodynamical (MHD) flow. To capture the dynamics of bubble nucleation, growth, coalescence and the interactions among bubble bath metal, each scale needs to be resolved with the appropriate method. The present study proposes a three-dimensional (3D) multiscale multiphase flow model for bubble behaviors and bath metal MHD flow, where the large-scale interfaces of bubble bath and bath metal are resolved by the volume of fluid (VOF) approach and the dispersed microbubbles are resolved by Lagrangian discrete bubble model (DBM). A discrete-continuum transition model is proposed to bridge different scales and handle the multiscale bubbles coexisting at the anode bottom. The predicted gas coverage and bubble thickness are validated by the experimental data in the literature. The numerical results indicate that bath metal MHD flow accelerates the bubble motion and decreases gas coverage.