High-resolution near-field three-dimensional (3D) radar imaging techniques with millimeter and terahertz wave have played an increasingly significant role in applications including hidden object detection and nondestructive testing. Currently, imaging methods suffer from low efficiency when imaging defects in stratified media. This is caused by the inadaptability of the fast Fourier transform in the frequency domain due to the alteration of wave numbers in different media. We propose an imaging method based on the nonuniform fast Fourier transform to overcome the problem. Numerical simulations and experiments were carried out to verify our idea. Results show that our proposed method can greatly improve the imaging efficiency while maintaining the imaging quality. This work is of great significance for future development of nondestructive testing technology based on millimeter wave/terahertz imaging.