Direct inversion of measured multiple-energy Kikuchi electron patterns from a Si(001) (2×1) surface with glancing and normal-incidence geometry shows clear images of the surface dimer and the bulk atoms. The three-dimensional artifact-free real-space images of the atoms contributed from different local emitters are resolved clearly. The observations demonstrate that Kikuchi electron holography has the surface sensitivity and can reveal the atomic structures of complicated multiemitter systems. By changing the collecting angle of Kikuchi electrons, one can selectively image the atoms behind the emitter in the backward direction; thus the surface and the bulk information can be obtained with different collecting angles. Therefore, the potential of Kikuchi electron holography to solve the local atomic structure of the unknown surfaces is high.