The predictions of flow structure, vortex shedding, and drag force around a circular cylinder are promoted by both academic interest and a wide range of practical situations. To control the flow around a circular cylinder, a magnetic obstacle is set upstream of the circular cylinder in this study for active controlling the separated flow behind bluff obstacle. Moreover, the changing of position, size, and intensity of magnetic obstacle is easy. The governing parameters are the magnetic obstacle width (d/D = 0.0333, 0.1, and 0.333) selected on cylinder diameter, D, and position (L/D) ranging from 2 to 11.667 at fixed Reynolds number Rel (based on the half-height of the duct) of 300 and the relative magnetic effect given by the Hartmann number Ha of 52. Results are presented in terms of instantaneous contours of vorticity, streamlines, drag coefficient, Strouhal number, pressure drop penalty, and local and average Nusselt numbers for various magnetic obstacle widths and positions. The computed results show that there are two flow patterns, one with vortex shedding from the magnetic obstacle and one without vortex shedding. The optimum conditions for drag reduction are L/D = 2 and d/D = 0.0333–0.333, and under these conditions, the pressure drop penalty is acceptable. However, the maximum value of the mean Nusselt number of the downstream cylinder is about 93% of that for a single cylinder.