Three-dimensional image reconstruction with Feldkamp, Davis, and Kress (FDK) algorithm is the most time consuming part in Micro-CT. The parallel algorithm based on the computer cluster is capable of accelerating image reconstruction speed; however, the hardware is very expensive. In this paper, using the most current graphics processing units (GPU), we present a method based on common unified device architecture (CUDA) for speeding up the Micro-CT image reconstruction process. The most time consuming filtering and back-projection parts of the FDK algorithm are parallelized for the CUDA architecture. The CUDA-based reconstruction speed and image qualities are compared with CPU results for the projecting data of the Micro-CT system. The results show that the 3D image reconstruction speed based on CUDA is ten times faster than the speed with CPU. In conclusion the FDK algorithm based on CUDA for Micro-CT can reconstruct the 3D image right after the end of data acquisition.