Distribution automation system is developing towards multi-function and intelligent direction. Among them, the Feeder Terminal Unit (FTU) based on the deep integration of primary and secondary devices is more susceptible to electromagnetic interference than traditional FTU due to the adoption of electronic sensors. However, few systematic studies of this kind of FTU on the anti-emi problems have been published. In this paper, the main electromagnetic interference modes and the conduction/coupling paths of FTU on column circuit breaker based on the deep integration of primary and secondary devices are analyzed in detail under four conditions: on-off operation of circuit breaker, single-phase grounding short-circuit fault, phase to phase short-circuit fault and lightning wave intrusion. Furthermore, a process-based design method of anti-emi for FTU of on-column circuit breaker is proposed, and the application paradigm of anti-emi design method proposed in this paper is illustrated by introducing the design process of anti-emi technology scheme of FTU based on ADCU+MCU structure.