Unmanned aerial vehicle (UAV) ground-penetrating radar (GPR) is an important research topic for target detection in many fields. In this paper, we develop a UAV-mounted GPR system with a frequency band at 150 MHz–309 MHz. However, the received signal in the complex background is covered by various clutter and interference, leading to the serious obscuring of the target. To meet this challenge, a cross-correlation-based background subtraction (CCBS) method and an interference suppression technique are adopted in combination for more accurate detection. The CCBS method processes the raw echo by establishing a background-removal model and using the similarity between each A−Scan and a reference wave. In addition, a Butterworth filter is adopted to get rid of the active electromagnetic interference beyond the working frequencies of the system; then, a lateral Doppler filtering (LDF) technique is introduced to suppress the passive interference generated by the rotation of the UAV rotor itself. Moreover, a practical method for estimating the dielectric constant is introduced by the calibration process of the measured radar echo. Numerical simulations and experimental results by our UAV-GPR system demonstrate that the proposed method has presented a better performance than the traditional methods, and the system has great potential in detecting deeply buried targets.