At present, frequency estimation algorithm based on DFT interpolation is widely used because of it’s high operation efficiency, but the estimating accuracy is dependent on the signal frequency, and for specific frequency, the estimation performance is bad. To solve this problem, a high accuracy frequency estimation algorithm with lower calculating complexity is proposed. In this algorithm, the signal frequency was estimated by Secant Method based on the DFT samples, and decimal fraction frequency of peak magnitude DFT sample was estimated to generate new DFT samples, thus reducing the DFT sample interval with little calculating burden, then improving the estimating accuracy. In addition, through removing the frequency reliant characteristics of estimation which exist in traditional frequency estimator based on the DFT interpolation, this algorithm increased the iterative estimation. To analyze the performance of the algorithm, a simulation was fulfilled. The simulation results show that the single frequency estimator without iterative estimation has asymptotic estimating variance less than 1.2 times the CRLB, which is better than the traditional frequency estimator based on the DFT interpolation, with calculation labor of N log₂N+2N complex multiplications, and the iterative frequency estimator has estimating variance about CRLB for all signal frequency calculation labor of N log₂N+2N complex multiplications, and N is the number of the DFT samples. 