Aiming to predict the electromagnetic compatibility (EMC) of a detection system on different working status correctly and quickly, the EMC prediction model based on effective amplitude is put forward. Firstly, according to the working principle of detection system, effective amplitude is defined, and the computation method of effective amplitude is given by amplitudefrequency response of matching circuit and bandpass filter circuit. Then, the three dimensional surface of effective amplitude is incised by the plane at the height of sensitivity, and the EMC boundary is obtained. Lastly, radiated interference is measured by electromagnetic measuring sensors. The conclusion that the detection system is electromagnetic compatible or not can be drawn with the help of the coordinate, which is decided by frequency and amplitude of radiated interference. Accuracy rate of the prediction model is 98.6% by experiment.