This paper reports the outline of the data acquisition system and the data compilatory program developed for geomagnetically conjugate observation of aurora and related phenomena being condcuted between three Antarctic stations and their geomagnetically conjugate stations in Iceland. The conjugate observation was initiated with Syowa (Antarctica)-Husafell (Iceland) pair in August 1983 and the observation was extended to other two pair stations of Mizuho (Antarctica)-Isafjordur (Iceland) and Molodezhnaya (Antarctica)-Tjornes (Iceland) in September 1984. The upper atmosphere physics data of the conjugate observation such as magnetic field, ULF, VLF and CNA have been continuously obtained in cooperation with Science Institute, University of Iceland. The recorded data are compiled using the computer system at the Information Processing Center, National Institute of Polar Research. The compilatory program has been developed in order to simplify the compilatory processes. A method of transformation from the digital data to physical units is also reported in this paper.