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With the principle of equivalent sampling and the application of full synchronization measurement theory, we use VHDL language designing a high-speed waveform acquisition system through FPGA chip EP1C6Q240C8, which not only overcome the shortcomings of poor time resolution of the real-time sampling systems, but also eliminates ±1 count error effectively. Our system can measure the frequency of waveform accurately and ensure the accuracy of acquired waveform. This paper gives the design method and simulation waveform of the high-speed waveform acquisition system. A system board can be made with the FPGA chip, which has higher practicability and reliability.