Acoustic noise and vibration of a BLDC motor is a coupled phenomenon between mechanical characteristics and electromagnetic origins through the motor air-gap. When a relative misalignment of rotor in the air-gap center exists on the assemblage, it is considered to influence the motor system characteristics. In this paper, the back electro motive force(BEMF) is analyzed by Finite Element Method(FEM) and verified by experiments for the SPM and IPM type motors. For magnetic field analysis, a FEM is used to account for the magnetic saturation. Using these results, the FEM is made to determine the appropriate electromagnetic field analysis in BLDC motors with rotor eccentricity ratio. A radial magnetic imbalance force of BLDC motor with rotor eccentricity is analyzed. Results demonstrate that the imbalance force is increased according to the degree of misalignment. An IPM motor, mostly chosen to realize high-speed operation, shows a worse effect on magnetic unbalanced forces and dynamic responses compared with SPM motor due to magnetic saturation when the rotor eccentricity exists.