The paper considers the problem of parameter identification of the surface mounted permanent magnet synchronous motor (SPMSM) with pulse width modulated (PWM) inverter in the presence of dead time of power switches and other nonlinear distortions. Parameter identification of the SPMSM is required for the tuning of the torque control loop, because in some cases, the exact values of phase resistances and inductances are not known. In the absence of nonlinear disturbances, the problem of SPMSM parameters estimation is not difficult. The influence of the dead-time effect, back electromotive force and measurements noise introduces distortions in experimental output data sets, which leads to incorrect parameter estimation. Thus, there is a need to develop new designs of identification experiments and methods of processing of the experimental data. A detailed mathematical model of SPMSM with a PWM inverter in the presence of dead-time effect is considered in the paper. The negative influence of the dead-time effect on the results of parameter estimation is shown. A modified technique of parameter identification of SPMSM based on the estimation of frequency response function is proposed. The applied design of identification experiments, the type of excitation input signal, and methods of data processing allow us to minimize the influence of nonlinear disturbances and to reduce the variance of estimation of frequency response function. These features provide a high performance of SPMSM parameters estimation.