The discrete Fourier transform (DFT) has become a main method of the harmonic analysis because it can be easily implemented in embedded system, but the conventional DFT is afflicted by the spectral leakage and the picket fence effect (PFE) in the asynchronous sampling. In this paper, the frequency-domain estimation method of the harmonic parameters, which is based on the windowing interpolated DFT (IpDFT) algorithm, is considered. In the modulus-based windowing IpDFT algorithm, a novel approach of frequency estimation error caused by the asynchronous sampling is proposed, and it is obtained by using the dichotomy approach algorithm. The proposed method can be easily carried out to solve the high order equations by microcontroller. In order to reduce the other harmonic measurement error caused by the fundamental component spectral interference, the rectification formula of frequency estimation error is derived for the Blackman window. The feasibility and validity of the proposed methods are confirmed by computer simulations and actual experiments of multi-frequency signals.