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This paper introduces a high speed data acquisition system based on NIOS II, especially focuses on the development process of NIOS II soft-core in data acquisition system. Acquisition data is transferred to computer for displaying and analysising by USB interface. Acquisition rate is 250MSPS, the real-time and low-pass filter is used as well, the acquisition data is stored in the RAM first, then processed by the NIOS II core, at last, the data was transferred to computer. The whole acquisition process is controlled by software on the computer. The experiment results show that the system have a good performance.