This paper studies the non-uniform air-gap caused by stator and rotor deformations, together with its effects on the spatial and temporal spectrum of the radial magnetic force density in an interior permanent magnet synchronous motor (IPMSM). According to the mathematical model of the deformed air-gap length, the superposition method is adopted to derive the air-gap permeance. Then, the formulas of the magnetic flux field and radial force density of the IPMSM considering air-gap deformation are obtained. Considering the stator oval deformation and the rotor centrifugal distortion in the electromagnetic finite element models (FEMs), the finite element analysis (FEA) and experiments of the investigated IPMSM are carried out to verify the results obtained by the theoretical analysis at different operations. Finally, the mathematical correlation between air-gap deformation and electromagnetic vibration is obtained. The result is helpful in solving problems of mutual influence between electromagnetic and mechanical characteristics during the optimization design of IPMSM.