Abstract: Frequency-domain interpolation is a widely used method for frequency estimation of multiple sinusoids. To improve the frequency estimation performance when the interval between adjacent frequencies is small, a new estimation algorithm based on two-stage windowed interpolation is proposed in this paper. In this algorithm, frequencies are estimated by a new interpolator which supports arbitrary windows. By choosing different windows in different stages, the proposed algorithm can reduce the mutual interference between multiple sinusoids without loss of signal-to-noise ratio. Numerical results show that the proposed frequency estimation algorithm has better estimation performance than the state-of-the-art algorithms, especially when the interval between adjacent frequencies is small.