To effectively remove microscale inclusions in the tundish, the Multi-Hole-Double-Baffles (MHDB), a novel flow control device in the tundish for continuous casting, was developed. The hole array mode of the MHDB will directly affect the trajectories of the inclusions. The effect and removal mechanism of the inclusions with sizes of 1 µm to 50 µm in the tundish with MHDB were studied by numerical simulation. The hole array mode of MHDB could affect the inclusions' trajectories and distribution, and the mechanism underlying the effect of the MHDB was investigated using the discrete phase model (DPM). A 1:2.5 physical model was built to verify the accuracy of numerical simulation. The results showed that micro-inclusions were primarily driven by the drag force exerted by the molten steel flow, micro-inclusion trajectories followed the molten steel streamlines almost exactly, but buoyancy still played a role in the removal of the micro-inclusions near the molten steel surface; the hole array mode affected the trajectories of the micro-inclusions and controlled and decelerated the flow of molten steel, increasing the residence time of the molten steel flow a the value that is 15 times larger than the theoretical value; and "upper-in-lower-out" type MHDB showed the most efficient removal of micro-inclusions, with the removal rate being increased by 13-49% compared to the removal rates for the other type MHDB. The results of numerical simulation were well verified by physical simulation.