Unmanned aerial vehicles (UAVs) equipped with magnetic airborne detectors (MADs) represent a new combination for underground or undersea magnetic anomaly detection. The electromagnetic interference (EMI) generated by a UAV platform affects the acquisition of weak magnetic signals by the MADs, which brings unique conceptual design difficulties. This paper proposes a systematic and integrated low-EMI design method for small, fixed-wing UAVs. First, the EMI at the MAD is analyzed. Second, sensor layout optimization for a single UAV is carried out, and the criteria for the sensor layout are given. To enhance UAV stability and resist atmospheric disturbances at sea, the configuration is optimized using an improved genetic algorithm. Then, three typical multi-UAV formations are analyzed. Finally, the trajectory is designed based on an analysis of its influence on EMI at the MAD. The simulation results show that the low-EMI design can keep MADs away from the EMI sources of UAVs and maintain flight stability. The thread-like formation is the best choice in terms of mutual interference and search width. The results also reveal the close relationship between the low-EMI design and flight trajectory. This research can provide a reference for the conceptual design and trajectory optimization of small, fixed-wing UAVs for magnetic anomaly detection.