Because of the advantages of simple construction, low cost of protection of unit length and wide detection range, the fiber perimeter intrusion detection has become a hot research field both at home and abroad. Positioning type vibration fiber detection machine outputs huge sensor array signals. The data volume is very large and needs high real-time processing requirement. Based on the locating optical fiber perimeter security system engineering project, NVIDIA's Compute Unified Device Architecture(CUDA) platform on Graphics Processing Unit(GPU) is utilized to accelerate preprocessing algorithm. The results show that the preprocessing algorithm can achieve a good acceleration on GPU, and improve the performance of the system obviously.