The space-based astronomy telescope will observe ultra-faint objects whose brightness should be lower than 23th magnitude.To ensure telescope performance,very low system noise requirements need extreme low CCD operating temperature(lower than-65℃).Because the satellite will be launched in a low earth orbit,inevitable space external heat fluxes will result in a high sink temperature(higher than-65 ℃).Only passive measures can't meet the focal plane cooling specification and active cooling technologies must be utilized.Based on detailed analysis on thermal environment inside and outside the telescope,thermal characteristics of focal plane assembly(FPA)etc.,active cooling system which is based on thermo-electric cooler(TEC)and heat rejection system which is based on flexible heat pipe and radiator have been designed.FPA prototype model has been developed and thermal balance test in vacuum conditions have been accomplished.Temperature distribution and variation of key parts and some important working parameters such as voltage and current of TECs in extreme cases have been acquired.Test results show that CCD can be controlled lower than-65 ℃ and all parts worked well during the test.All of these verified the validity of thermal design of FPA and some lessons will be presented in this paper.