The invention relates to a frequency domain imaging method of a ground penetrating radar, which is a frequency domain imaging algorithm based on linear frequency modulation waves. The method comprises the steps of performing difference frequency treatment on a target echo signal received by the radar and a reference signal, obtaining an echo wave after the difference frequency; performing Fourier transform on a two-dimensional scanning direction of the echo wave; and then performing phase compensation on data by taking an imaging central point as a reference point; then, performing secondary slot interpolation operation; decoupling three-dimensional imaging data by the slot interpolation; and finally, performing three-dimensional Fourier transform on data after slot interpolation, thereby accomplishing reconstruction of images. According to the frequency domain imaging method of the ground penetrating radar, the problem in three-dimensional coherent imaging under near field condition is solved, and compared with a conventional pulsed incoherent imaging technology, and images with better resolution ratio can be obtained.