Ion heating effect incuced by near-field thermal noise of superconducting ion chip at different temperature is investigated based on fluctuation-dissipation theorem. The approximate expressions of electric field fluctuation spectral density under different conditions are obtained by the electric field Green function and multi-layer reflection coefficients. For pure Nb electrode, the near-field thermal noise spectral density is inversely proportional to the electrode thickness when the temperature T is 295 K. The near-field thermal noise spectral density is irrelevant with the electrode thickness when T is 4 K, and the near-field thermal noise can be reduced by over ten orders of magnitude comparing to the case of room temperature. The case that there are Nb2O5 thin films on the surface of niobium electrode is analyzed. Results show that the electric field fluctuation induced by Nb2O5 film occupies the main position. The noise spectral density is proportional to the Nb2O5 thickness. When chip temperature decreases to 4 K, the thermal noise decreases by 5 to 6 orders of magnitude.