Abstract: Microwave amplifier is one of the key components of signal generator system used in radar, communication, navigation and so on. With greater requirements for high power, miniaturization, integration and reliability, the thermal performance of high power amplifier gradually becomes a main factor limiting its further developments. Based on CFD software Flotherm, thermal design of a Ku-band multiplex high power microwave amplifier are carried out in this paper. Basic theories of heat transfer are discussed. Cooling system design of the amplifier and thermal structure design of its cavity are carried out. The structure and size of the heat sink is optimized at last. Eventually, steady thermal analysis of the amplifier is carried out at the ambient temperature of 35 ℃, the temperature of amplifier chips and the air flow speed of cooling fans are obtained, it reveals that the thermal design of this amplifier satisfies its thermal requirements.