This study assessed the survivability of an engine control system under intense electromagnetic pulses. It investigated the electromagnetic sensitivity of the system under the action of intense electromagnetic pulses. In this work, the evaluation focuses on the terminal circuit of the control system. It proposes a co-design method for electromagnetic pulse protection circuits on a printed circuit board. The electromagnetic interference mechanism and phenomena were analyzed through simulation and experiments. The electromagnetic susceptibility of the control system was tested using the bulk current injection test method, and the pulse coupling signal of the sensitive part was obtained. Subsequently, the terminal circuit was analyzed using a numerical calculation method. The pulse coupling signal was injected into the terminal circuit. Thus, we can determine why the control system exhibits sensitive phenomena. Then, a protection circuit of the terminal circuit was established. The design method's advantage is accurately locating the circuit's sensitive points and reducing the controller circuit's electromagnetic sensitivity by designing the circuit without drastically changing the original circuit. At the same time, the redundancy of protection circuit design can be effectively reduced.