Magnetic fluid seal is characterized by its simple design, low friction and being dustless. Those advantages are deduced from the fact that the sealing element is not a solid such as rubber or plastic but it is a fluid. Those are critical for application to a rotating shaft which is inserted into a vacuum chamber where high level of vacuum and cleanness are required. For the reason the magnetic fluid seal has become a standard for vacuum chambers for semiconductor and LCD processing. It should be noted that its sealing performance is sensitive to temperature. If necessary, water cooling should be considered. Thus anticipation of the temperature distribution of the magnetic fluid seal is important before applying it. In this paper an FEM analysis of the heat transfer has been executed and compared with experimental results. An overall convective heat transfer coefficient has been adopted for the analysis, which results in satisfactory consistency of the theoretical and experimental results.