The present invention discloses an IpDFT(Interpolation Discrete Fourier Transform)-based frequency estimation method of a non-equilibrium electric power system. The problem of non-circular signal employed frequency estimation in a non-equilibrium condition is solved based on modeling of complex-valued signals deduced from a three-phase voltage through orthogonal [Alpha][Beta]transformation. The newest progress obtained through enhanced complex-valued second-order statistics is employed, and in a non-equilibrium condition, the complex-valued signals are second-order non-circular signals. In theinvention, interpolation Fourier transform is employed to estimate frequency of the signals, the non-circular signals are converted to sinusoidal signals through simple calculation, positive and negative frequency components are considered, and therefore, the estimation accuracy of the frequency is improved and the calculation is simple. Compared to traditional linear adaptive estimation, the method is more suitable for the non-equilibrium system, gives out unbiased frequency estimation, and is not sensitive to frequency change. The method is more stable and low in calculation complexity, andis improved in robustness anti-noise performance and estimation precision.