In this paper, the annual variation characteristics of each channel at 404 stations were analyzed by using the observation data of ZD8MI multi-separation array observation system from June 2018 to June 2020. It was found that the annual variation characteristics of each channel were different with the difference of observation pole distance. The experimental observation at different polar distances and the simulation analysis of annual change showed that the change of shallow resistivity is relatively large, while the change of deep resistivity is relatively small. The annual variation of 404 station is caused by the seasonal variation of shallow medium resistivity with temperature. The phase difference of annual variation form of different channels is caused by the variation of shallow medium resistivity at different depths. Therefore, the observation of earth resistivity at different depths by using the multi-separation array observation system is particularly important to quantitatively identify the surface non-seismic interference.