The Magnetic fluid is a new type of magnetic material. It is a colloidal liquid made of nanoscale ferromagnetic particles suspended in a carrier fluid. Magnetic fluid sealing is one of the most successful applications of the magnetic fluid. As a new type of seal with the advantages of no leakage, long life and high reliability, magnetic fluid seal has been widely used under vacuum and low pressure differential condition. Two types of permanent magnets, the annular permanent magnets and the cylindrical magnets, are usually used in magnetic fluid seals in engineering. However, the influence of permanent magnet structure on sealing capacity was not clear, hence a new experimental setup was designed in order to study the influence of permanent magnet structure on sealing capacity. The annular permanent magnets and the cylindrical magnets were used as the magnetic source of the experimental setup in a series of tests respectively. The relationship between the sealing capacity of magnetic fluid seal and the end-face area, axial length of the magnet was analyzed by the electromagnetism theories and theoretical derivation. The result of the experiments shows that the sealing capability grows with the end-face area of the magnet, and the growth rate becomes much slower when magnet end-face area attains a certain value; the reluctance of pole pieces and shaft can’t be ignored when magnetic field attains a certain value; the modified theoretical formula had a good match to the measured values when the end-face area of the magnet is small enough to ignore the reluctance of pole pieces and shaft.