To get rid of the interference of electronic noise in the micro channel plate photon counting imager detector, the theory of partition noise was studied and the finite element method of calculating partition noise by COMSOL software was proposed. The three dimensional model of imaging principle based on the Vernier anode detector was built, the image of a set of pinhole array was simulated, and the centroid position offsets caused by the partition noise were calculated, which certifies the correctness of the position decoding algorithm and proves the feasibility of calculating partition noise. By adjusting the designed parameters of the Vernier anode, the influences of the partition noise on the centroid position offset of charge cloud were investigated. It is an effective way to reduce the partition noise by increasing the gains of micro-channel plates.