This paper presented a real-time endoscope ultrasonic digital imaging system, which was based on FPGA and applied for gastrointestinal examination. Four modules, scan-line data processing module, coordinate transformation and interpolation algorithm module, cache reading and writing control module and transmitting and receiving control module were included in this FPGA based system. Through adopting different frequency ultrasound probes in a single insertion of endoscope, the system showed a high speed data processing mechanism capable of achieving images with various display effects. A high-precision modified coordinate calibration CORDIC (HMCC-CORDIC) algorithm was employed to realize coordinate transformation and interpolation simultaneously, while the precision and reliability of the algorithm could be greatly improved through utilizing the pipeline structure based on temporal logic. Also, system real-time control by computer could be achieved through operating under the condition of USB2.0 interface. The corresponding experimental validations proved the feasibility and the correctness of the proper data processing mechanism, the HMCC-CORDIC algorithm and the USB real-time control. Finally, the specific experimental sample, a tissue mimicking phantom, was imaged in real-time (25 frames per second) by an endoscope ultrasonic imaging system with image size 1024×1024. The requirements for clinical examination could be well satisfied with the imaging parameters discussed above.