Large-eddy simulation (LES) of turbulent MHD duct flows is carried out in the liquid metal MHD generator, and the influence of the non-uniform magnetic flux density on the turbulent flows is examined. For high magnetic flux density, the structures of Reynolds stress align along the orientation of the magnetic flux density, and those structures periodically flowed toward the downstream region like Karman vortex sheets are observed. The stronger magnetic field makes the laminarized flow turbulent again. That is confirmed by using spectrum analysis. It is found that a pair of eddy as the secondary flow for the non- MHD duct flow diminishes in the MHD flow. The non-uniform magnetic flux density in the streamwise direction produces the eddy currents that lead to the M-shaped velocity profiles in the plane parallel to the external magnetic field. The velocity profiles are modulated more strongly with the magnetic flux density.