According to the principle of Vernier anode photon counting detector, in this paper we discuss a decoding algorithm of calculating centroid location and interelectrode capacitance between electrodes, which has a close relationship with preamplifier circuit noise. Based on the Poisson's equation, the theoretical model of Vernier anode is established. The method of calculating the irregular shape uniplanar self-capacitance and interelectrode capacitance between electrodes using ANSYS finite element analysis is introduced. In addition, a Vernier anode plate is manufactured with picosencond laser micromachining process on a 1.5 mm thick quartz substrate with gold film as conductors. The Vernier anode pattern has a picth of 9.9 mm, an active area of 19.8 mm×19.8 mm, insulation channel depth of 10 μm, and insulation channel width of 30 μupm. Comparing the simulated capacitances with the measured capacitances, the validity of the three-dimensional finite-element method is proved. A simulation study on the effects of substrate permittivity, insulation channel width and depth on capacitance change is carried out. The simulation result provides a basis for structure design of Vernier anodes.