Abstract: The radiation risk is the key problem to the spacecraft which used the plutonium-238 heat source. Radiation risk assessment includes large amounts of data analysis and evaluation methods establishment, involving heat source safety design, launch analysis and radiation dose estimation. Taking the Chang’e 3 for example, this paper puts forward the radiation risk assessment methods, processes and calculation result of this mission. At the same time, it can be used to guide the radiation risk assessment of domestic space missions which carry nuclear energy.