The heater structure plays an important role in the chip-scale atomic clock (CSAC) to achieve the performance of low power consumption, and it is the most effective way to make the structure by depositing the indium tin oxide (ITO) for its heating performance and transparent property. The influence of the factors, including the RF power and the depositing pressure in the fabrication process, on the characteristics of the ITO film is investigated first in this paper. Then the key properties of the ITO film such as the depositing rate, the resistivity, the sheet resistance and the transmittance are tested. The depositing rate is tested by an AlphaStep D-100, the resistivity and the sheet resistance are measured using a four-probe method, and the transmittance is analyzed with a spectrophotometer U-4100. Based on the properties tested above, the optimized process parameters with an RF power of 70W, a substrate under room temperature and a depositing pressure of 0.2Pa are chosen to fabricate the heater structure. Finally, a heater structure with 60ohm resistance is designed and fabricated. Test results show that the heater structure can heat the physics package of the CSAC up to 85 o C in less than 420 seconds, which is suitable to be used in the CSACs.