A space-borne differential optical absorption spectrometer is a high precision aerospace optical remote sensor. It obtains the hyper-spectral，high spatial resolution radiation information by using the spectrometer with CCD（Charge Coupled Device）array detectors. Since a few CCDs are used as the key detector, the performance of the entire instrument is greatly affected by working condition of CCDs. The temperature of CCD modules has a great impact on the instrument measurement accuracy. It requires strict temperature control. The selection of the thermal conductive filler sticking CCD to the radiator is important in the CCD thermal design. Besides，due tothe complex and compact structure, it needs to take into account the anti-pollution of the optical system. Therefore, it puts forward high requirements on the selection of the conductive filler. In this paper, according to the structure characteristics of the CCD modules and the distribution of heat consumption, the thermal analysis tool I-DEAS/TMG is utilized to compute and simulate the temperature level of the CCD modules, while filling in thermal grease and thermal pad respectively. The temperature distribution of CCD heat dissipation in typical operating conditions is obtained. In addition, the heat balance test was carried out under the condition of two kinds of thermal conductive fillers. The thermal control of CCD was tested under various conditions, and the results were compared with the results of thermal analysis. The results show that there are some differences in thermal performance between the two kinds of thermal conductive fillers. Although they both can meet the thermal performance requirements of the instrument, either would be chosen taking account of other conditions and requirements such as anti-pollution and insulation. The content and results of this paper will be a good reference for the thermal design of the CCD in the aerospace optical payload.