Conformal coatings are essential for ensuring the reliable operation of printed circuit boards (PCBs) in complex environments, effectively preventing external corrosion and component aging. However, current conformal coating detection techniques remain inadequate, making it difficult to achieve comprehensive coverage assessment, which affects the coating’s protective capability and long-term stability. This paper proposes a PCB conformal coating coverage detection method based on electromagnetic scanning and fluctuation sequence difference measurement. First, the electromagnetic shielding mechanism of the conformal coating is analyzed, providing a theoretical foundation for system detection. Next, an improved adaptive fluctuation sequence difference measurement method is proposed. This method acquires electromagnetic radiation data of the PCB under normal and weakened coating conditions through near-field scanning, applies wavelet decomposition for noise reduction, and uses an improved difference measurement algorithm to calculate the distance between two fluctuation sequences to identify coating defect areas. Finally, the effectiveness of this method is verified through simulations and experimental measurements. The results demonstrate that this method significantly enhances the accuracy and reliability of coating detection, overcoming limitations in traditional coating assessment methods and offering new perspectives for the theoretical research and engineering applications of electromagnetic shielding technology.