In order to improve the reconfigurability and computing efficiency of the polyphase channelization system, a new algorithm based on CUDA stream architecture was designed and optimized. Firstly, the principle of parallel channelization algorithm without blind zones is introduced. Then, various resource constraints under CUDA architecture and the relationship between the operating efficiency and parameters of the CUDA kernel under these constraints are analysed. The implementation structure of polyphase channelization algorithm is designed. Finally, NVIDIA GPU is used to implement and test the polyphase channelization algorithm based on CUDA stream. The result proves that the computational efficiency of the structure designed in this paper meets the real-time requirements, and can get about 10% efficiency improvement compared with the traditional algorithm.