The atomic configurations of segregated B atoms on a highly B-doped Si(001) surface is investigated with scanning tunneling microscopy (STM) observation and first-principle cluster calculation, on which characteristic comb-shape step structures are observed. The characteristic features in the STM image are (1) dark regions in the occupied state, and (2) paired protrusions in the unoccupied state. The calculation shows that models of a B dimer on the top surface and B atoms bonded to two neighboring Si atoms in a dimer row can reproduce STM images well for (1) and (2), respectively. ©1997 American Institute of Physics.