Channel materials and environment in communication system will affect the phase of RF signal. Aiming at the problems of low calibration frequency and large error in traditional phase calibration methods, a phase difference calibration method based on software radio technology is proposed. The phase value of the maximum spectral line is solved by the fast Fourier transform and the coordinate rotation digital computer, and the phase calibration of the signal is completed by combining the digital orthogonal technique. The method was tested experimentally with the billiongate FPGA as the core. Xilinx Artix7 was used to generate reference and to be calibrated signals, and logic circuits such as DDR3 storage, phase difference measurement and calibration of billiongate FPGA were designed to complete phase difference calibration. The test results show that the relative error of phase difference is less than 03% and the rootmeansquare error is only 007° for radio frequency signals with a frequency of 1 GHz in the range of -90° to 90°.