The invention relates to a target missile assembly detection system and a method. The system comprises an oscillograph, a PIN modulator, a voltage controlled oscillator, a power amplifier, a circulator, a detecting head, a microwave unreflected chamber and an antenna, wherein the antenna extends into the microwave unreflected chamber from the antenna mounting port of the microwave unreflected chamber. The method comprises the following steps: after the amplitude-modulated waves, which are emitted by the antenna, are reflected by a luneberg lens in a target missile and are received by the antenna, inputting the waves to the detecting head by the circulator to detect the amplitude; inputting the detection result to the oscillograph to be displayed, thereby obtaining the oscillograph output level which reflects the position of the luneberg lens of the detected target missile; checking whether the oscillograph output level is within the range of 160-195 mV; if so, judging that the luneberg lens is placed in a proper position; and if the level is equal to the critical values of the range or beyond the range, judging that the luneberg lens is not placed in the proper position. The invention can be used for effectively detecting whether the luneberg lens is placed in the proper position on the target missile. The system has the advantages of compact structure, light weight, low cost and stable detection performance.