We present the spatial resolution estimation methods for a photon counting system with a Vernier anode. A limiting resolution model is provided according to discussions of surface encoding structure and quantized noise. The limiting resolution of a Vernier anode is revealed to be significantly higher than that of a microchannel plate. The relationship between the actual spatial resolution and equivalent noise charge of a detector is established by noise analysis and photon position reconstruction. The theoretical results are demonstrated to be in good agreement with the experimental results for a 1.2 mm pitch Vernier anode.