Mathematical models are disappointing due to uneven distribution of the air gap magnetic field and significant unmodeled dynamics in magnetic bearing systems. The effectiveness of control deteriorates based on an inaccurate mathematical model, creating slow response speed and high jitter. To solve these problems, a model-free adaptive control (MFAC) scheme is proposed for a three-degree-of-freedom hybrid magnetic bearing (3-DoF HMB) control system. The scheme for 3-DoF HMB depends only on the control current and the objective balanced position, and it does not involve any model information. The design process of a parameter estimation algorithm is model-free, based directly on pseudo-partial-derivative (PPD) derived online from the input and output data information. The rotor start-of-suspension position of the HMB is regulated by auxiliary bearings with different inner diameters, and two kinds of operation situations (linear and nonlinear areas) are present to analyze the validity of MFAC in detail. Both simulations and experiments demonstrate that the proposed MFAC scheme handles the 3-DoF HMB control system with start-of-suspension response speed, smaller steady state error, and higher stability.