An ocean bottom electromagnetic receiver (OBEM) is primarily designed to measure the submarine electromagnetic signal. In order to verify the function of the instrument and improve the accuracy of result, the instrument is self-checked by a built-in channel calibration before OBEM enters the water. OBME-Ⅲ needs to export the calibration file generated by channel calibration from the instrument, and then use the Matlab program on the PC side to perform calibration calculation, which has shortcomings such as complex offshore operations and low calculation efficiency. In order to solve these problems, the author developed a calibration calculation program based on the ARM-Linux platform. By entering the relevant commands, the channel calibration calculation can be realized locally in OBEM-Ⅲ, reducing the trouble of exporting data for calculation on multiple platforms. The mixed-base fast Fourier transform calculation method adopted reduces the calculation time from 90 s to 11 s while ensuring the calculation accuracy, which greatly improves the calculation speed and improves the efficiency of the instrument's offshore operations. In the magnetotelluric scientific research mission carried out in the southwest of the South China Sea from July to August 2020, the program performed well and successfully obtained high-quality submarine magnetotelluric sounding data.