This paper deals with the cogging torque analysis of a BLDC Motor, which has the axial displacement of its rotor. In order to improve the torque performance of the BLDC motor, Brushless motor is commonly designed to minimize its cogging torque. Therefore, a skewed model is used to reduce the cogging torque. However, even though the rotor or stator is skewed, the cogging torque could be increased by the axial displacement of the rotor, which occurs when the BLDC Motor is manufactured. Therefore, this paper investigates the effect of the axial displacement of the rotor on the cogging torque. In order to investigate the effect, an analysis method, which is 3D-EMCN in combination with 2D-FEM, is proposed to analyze the cogging torque of the BLDC motor with the axial displacement of its rotor, and the result of the analysis is verified by comparison with the experimental result.