CubeSats for deep-space applications are becoming increasingly popular and successful. The aim of this thesis, developed in collaboration with the Italian space company Argotec, is to present the analysis methodologies and design options available on this category of satellites for thermal control. To do this, two missions used as case studies will be presented: LUMIO (Lunar Meteoroid Impact Observer) and HENON (HEliospheric pioNeer for sOlar and interplanetary threats defeNce). HENON and LUMIO missions are pioneering deep-space projects employing 12U CubeSat platforms. HENON aims to advance space weather forecasting by placing a CubeSat in a distant retrograde orbit (DRO) around the Earth, providing early warning signals for solar events.