Harmonic leakage inductance occupies a high proportion in the synchronous inductance of fractional slot concentrated winding permanent magnet synchronous motor (FSCW‐PMSM), and the synchronous inductance determines the operating performance of the motor. To calculate the harmonic leakage inductance and synchronous inductance of the FSCW‐PMSM fed by inverters, two‐dimensional finite element analysis and the analytical method are used to study the influence of time‐harmonic current on the harmonic leakage inductance of the three‐phase FSCW‐PMSM in this study, and the influence mechanism is revealed. The relationship between the time‐harmonic magnetic field and space harmonic magnetic field is obtained, and the harmonic leakage coefficient and the working harmonic coefficient with different slot‐pole combinations are investigated. The results show that the time‐harmonic current can reduce the harmonic leakage inductance and increase the magnetising inductance, but has little effect on the synchronous inductance under the unsaturated condition. A prototype was manufactured and tested to verify the accuracy of the analysis model. The research results provide beneficial help for the design of the three‐phase FSCW‐PMSM fed by inverters.