Evolution of surface relief and its intrinsic mechanism associated with martensitic transformation (MT) during heating and cooling in Mn79.5Fe15.6Cu4.9 high-temperature antiferromagnetic shape memory alloy (SMA) have been investigated in nano-scale by means of in-situ atomic force microscopy (AFM), X-ray diffraction (XRD), and dynamic mechanical analyzer (DMA). Experimental results show that the N-type surface relief originates from the reverse MT and is completely made of matrix which is different from the conventional ones. The reverse MT exhibits untwinning shear and the reverse shearing of twinned martensites mainly contribute to the surface relief. The measured surface relief angles are less than 1°, which are determined by the small difference of lattice constants between fcc and fct structures. Surface relief has a good recovery property because of the crystallographic reversibility rule in SMAs, implying that this kind of alloy has a good surface morphology memory effect.