The morphology and crystalline structure of Er silicide nanocrystals self-assembled on the Si(001) substrate were investigated using scanning tunneling microscopy (STM) and transmission electron microscopy (TEM). It was found that the nanowires and nanorods formed at 630 °C has dominant hexagonal AlB(2)-type structure, while inside the nanoislands self-organized at 800 °C the tetragonal ThSi(2)-type structure is prevalent. The lattice analysis via cross-sectional high-resolution TEM demonstrated that internal misfit strain plays an important role in controlling the growth of nanocrystals. With the relaxation of strain, the nanoislands could evolve from a pyramid-like shape into a truncated-hut-like shape.