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Heart failure is one of the major diseases threatening human life. As a transitional support treatment before heart transplantation, left ventricular assist device has significantly improved the quality of life and survival rate of patients with end-stage heart failure. In the automatic detection of ECG, the detection of QRS complex is the most critical link, which affects the correctness and accuracy of subsequent data analysis and processing. This design uses the database data and human ECG acquisition data as the original source to be processed, the data is processed through the combination of high-order low-pass filtering and Shannon energy's innovative algorithm, and adds the use of high-order adaptive median filter algorithm on hardware to minimize the noise of the processed real-time data and facilitate the accurate extraction of R wave. Finally, the tested ECG R wave is used to drive the left ventricular assist device, after successful simulation by MATLAB and Modelsim software, the scheme of real-time ECG signal controlling blood pump system is realized on FPGA hardware. This method has been tested for accurate R-wave extraction and the ability to control the left ventricular assist device for simultaneous pumping.