Focusing on the problem of the accurate frequency estimation of complex sinusoidal signals, a flexible and reliable harmonic frequency estimation algorithm has been proposed. To ensure the flexibility of the algorithm, a new type of window (GMSDSMC-Hp,q) with adjustable number of function terms, multiplication orders and convolution orders was designed. Combined with the four-spectral-line interpolation algorithm, it can accurately estimate the frequency parameters of the power system. For the white noise background, a statistical description model of the frequency estimation results was established based on the law of uncertainty propagation, providing a basis for theoretical analysis. The experimental results show that the theoretical results of the frequency estimation variance are in good agreement with the Monte-Carlo simulation results, verifying the correctness and feasibility of the expression.