Magnetic fluid sealing technology is widely used in vacuum and gas sealing applications, due to its high reliability, “zero” leakage, and long service life. The magnetic fluid seal gap is uniformly distributed under ideal conditions. However, the bearing clearance and magnetic field forces can be generated by the permanent magnets in the magnetic fluid seal in actual operating conditions. The shaft can cause the radial runout, and shift to one side during rotation, leading to an uneven seal gap on the sealing performance and rotational torque. This paper first simulates and analyzes the influence of eccentricity on the magnetic induction intensity within the sealing gap, followed by experimental studies on the effects of eccentricity and sealing gap on sealing pressure resistance and rotational torque. The results indicate that the magnetic induction intensity within the sealing gap exhibits axisymmetric distribution along the eccentricity direction, and the magnetic field gradient at the maximum gap decreases, as eccentricity increases; When the eccentricity increases from 0 to 0.15 mm, the maximum pressure resistance of each group of pole shoes decrease by 17% to 84.6%; the smaller the theoretical sealing gap is under the same eccentricity, the more significant the decrease in pressure resistance is; the torque is exponentially proportional to the eccentricity, and when only the gap effect is considered, the torque is approximately inversely proportional to the minimum gap (with an error of 7.88%). This finding provides a theoretical basis for the anti-eccentricity design of magnetic liquid seals, indicating the significant impact of eccentricity on seal pressure resistance and torque. It also offers engineering references for the radial runout in the main shaft of magnetic liquid seals.