The 3D imaging microwave altimeter is a proposed instrument for obtaining centimeter level accuracy of topography for ocean and meter-level accuracy of topography for land. In order to ensure the normal operation of the system and improve its performance, the EMI and EMC problems should be considered in design phase. In this paper, the architecture of altimeter system is shown and the main EMI sources in the system are pointed out. According to the characters of EMI sources, EMC design for RF circuit and some key components including TWTA, high-speed AD converter and ICs is outlined.