Secondary electron yield (SEY) due to electron impact depends strongly on surface topography. The SEY of copper samples after Ar-ion bombardment is measured in situ in a multifunctional ultrahigh vacuum system. Increasing the ion energy or duration of ion bombardment can even enlarge the SEY, though it is relatively low under moderate bombardment intensity. The results obtained with scanning electron microscopy and atomic force microscopy images demonstrate that many valley structures of original sample surfaces can be smoothed due to ion bombardment, but more hill structures are generated with stronger bombardment intensity. With increasing the surface roughness in the observed range, the maximum SEY decreases from 1.2 to 1.07 at a surface characterized by valleys, while it again increases to 1.33 at a surface spread with hills. This phenomenon indicates that hill and valley structures are respectively effective in increasing and decreasing the SEY. These obtained results thus provide a comprehensive insight into the surface topography influence on the secondary electron emission characteristics in scanning electron microscopy.