There are problems of poor anti-interference capability and significant measurement accuracy degradation under frequency offset of the harmonic estimation algorithm based on the discrete Fourier transform (DFT). To address this issue, a harmonic phasor estimation method considering frequency deviation and harmonic interference is proposed. First, parameter information on the fundamental phasor is accurately obtained by a filter bank and an interpolated discrete Fourier transform (IpDFT) algorithm. Then, the passband center of the filter bank is corrected based on the fundamental frequency offset and uses the corrected filter bank and IpDFT to obtain the initial estimation of the harmonic phasors. Finally, the initial estimation of the IpDFT is corrected by amplitude and phase compensation to achieve accurate harmonic phasor estimation. Simulation results demonstrate that the proposed method can provide a frequency error below 5 mHz and a total vector error below 1% for all harmonic phasors from the first to the fiftieth order in various scenarios including frequency offset, harmonic distortion, noise interference, and multiple disturbances, based on the IEC 60255-118-1 standard.