The invention provides a bed load transport rate measurement system and method based on a cross correlation method. The measurement system comprises a water depth sounding device and a shore-based control device, wherein the water depth sounding device comprises a depth sounder hull, the depth sounder hull is mounted above an anti-collision floating ring through a supporting rod, and the bottom portion of the anti-collision floating ring is equipped with a pusher. The measurement method comprises steps that the section is measured through combination of field survey and remote sensing image design, and the measurement route of the water depth sounding device is set; continuous vertical underwater terrain measurement of a preset river section at two different time periods is carried out bythe water depth sounding device; the underwater terrain data is transmitted to the shore-based control device in a wireless mode, the sand wave moving speed and the average sand wave height are acquired through a terrain data analysis unit of the shore-based control device; the sand wave moving speed and the average sand wave height are substituted into a formula to acquire the single wide bed load transport rate, and observation and analysis of the bed load transport rate without disturbing the bed load transport process of natural river beds can be realized.