Horizontal karst caves were frequently studied for geohazards prospecting in the past. In this paper, the application of GPR to vertical karst caves was introduced in Zhangjiajie-Huayuan Expressway of Hunan Province, and the effectiveness of the complex signal analysis was illuminated in GPR data processing. A vertical karst cave characterized by a small horizontal scale would arose an unintelligible anomaly in the GPR image, which could not be recognized easily. The authors first processed the GPR data by two-dimensional spatial filter, and then applied Hilbert transform to the data, thus obtaining the transient amplitude, transient phase and transient frequency. Finally, the authors analyzed the processed data synthetically. The results show that the spatial filter can remarkably eliminate high frequency noise and improve SNR of the signal. In addition, the accuracy of the GPR interpretation can be improved by the multi-parameter analytical method. Drilling results prove the correctness of the inversion interpretation.