In this paper, we express a concept that the complete reconstruction process should include the computation part on GPUs and the data storage part. We propose a multi-thread scheduling (MTS) method to implement the FDK algorithm, to coordinate?? the computing and storage time. In this method we use multi0-threads to control the GPUs and a separate thread to accomplish data storage, so as to cover the calculation and data storage in time process. In addition, we use the four-channel texture to maintain symmetrical projection data in CUDA framework, which can reduce the calculation time significantly.. Numerical experiment shows that the time cost of the whole process with our method is almost the same as the data storage time cost.