The phase-locked amplification technique used in the general weak signal detection method is still difficult for high frequency short pulse signal. For the general phase-locked amplifier, the short pulse signal cannot reach the establishment time of the post-stage filter of the phase-locked amplifier, so it’s difficult to detect the weak high-frequency short pulse signal. Considering that the nonlinear ultrasonic signal is periodic signal, add digital average to the front stage of the phase-locked amplifier to increase the signal-to-noise ratio of the signal. According to the principle of best matching, the window length of the moving mean filter is set equal to the pulse duration, so as to realize the low-pass filtering only for the pulse signal, avoiding the problem that the common low-pass filter does not have enough time to establish the short pulse signal, and finally realizing the phase-lock amplification of high-frequency nonlinear short pulse signal detection. The system uses mixed digital analog circuit, and the logic algorithm deployed on the FPGA. The weak signal transmitter and computer are used to build a test platform to test the system. The test results show that the system can detect the pulse signals with a pulse length of 5 μS and amplitude of 100 nV when the input signal frequencies are respectively 0.6, 1, 2, 5 and 10 MHz, and has good linearity. Select the signal with frequency of 1 MHz for different pulse width test, the system can accurately detect pulse signals with pulse length of 5, 10, 30 μS and amplitude of 100 nV.