With the use of a newly developed spin-polarized scanning electron microscope, we have succeeded in obtaining the real-space images of the layered-antiferromagnetic state concurrent with 1-nm-stepped atomic terraces in layered-structure manganite La1.4Sr1.6Mn2O7. The three-dimensional analysis of spin alignment could further reveal the temperature-dependent spin reorientation and the anfiferromagnetic domain walls on the atomic terraces. These ensure the use of the present microscopy for quantitative analysis of local magnetic structures in a broader range of materials, including magnetic oxides and nanomaterials.