Recently discovered magnetic van der Waals (vdW) materials provide an ideal platform to explore low-dimensional magnetism and spin transport. Its vdW interaction nature opens up unprecedented opportunities to build vertically stacked heterostructures with novel properties and functionalities. By engineering the planar structure as an alternative degree of freedom, herein we demonstrate an antisymmetric magnetoresistance (MR) in a vdW Fe3GeTe2 flake with a step terrace that breaks the planar symmetry. This antisymmetric MR originates from a sign change of the anomalous Hall effect and the continuity of the current transport near the boundary of magnetic domains at the step edge. A repeatable domain wall due to the unsynchronized magnetization switching is responsible for this sign change. Such interpretation is supported by the observation of field-dependent domain switching, and the step thickness, temperature, and magnetic field orientation dependent MR. This work opens up new opportunities to encode magnetic information by controlling the planar domain structures in vdW magnets. [Figure not available: see fulltext.]