We provide the ghosting theory of two-dimensional Vernier anode based imagers. The single photon counting detection system based on Vernier anode is constructed. The ghosting, which occurs during the decoding of two-dimensional Vernier anode, and its possible solutions are described in detail. On the basis of the discussion of the decoding algorithm, the ghosting theoretical model is established. Phase conditions on which imaging ghosting can be avoided and the probability distribution function are proposed; the root causes of ghosting of two-dimensional Vernier anode are also discussed.