Blood flow velocity detection is important for clinical medicine. An FPGA based system of ultrasonic pulsed wave Doppler was proposed to measure blood flow velocity profile. A LiNbO3 piezoelectric transducer was used as the probe to produce and receive ultrasonic pulses. The ultrasonic pulse recurrence frequency was controlled by FPGA. The conventional analog mixer was eliminated by the digital quadrature demodulator based on Hilbert transform for the echo signal demodulation. The spectrum analysis was realized in FPGA through the fast Fourier transform. The experiment verified that the proposed system can measure the velocity profile in blood vessel with the deviation of less than 7%.