In order to meet the modern acoustic positioning system performance test requirements, the paper designs a high speed multi-channel signal generator based on PCI-E bus. Using the PC to generate different electric analog signal and generating board through PCI-E bus board output to the signal, it realizes the signal transmission of high-speed stability; Taking FPGA as the core controller, and achieve local bus conversion using PCI9054 bridge-chip, finally it complete the multi-channel signal waveform output through the DA logic control and multi-channel analog circuit conditioning. The system function is stability, and meets the requirements by the experimental test. The design has the simple structure, strong scalability, and the broad application prospect, and has been successfully applied to function of the laboratory detection of underwater acoustic positioning system.