Ionospheric phase decontamination is the key factor to improve the target detection capability of skywave radar. In this paper, a new ionospheric phase decontamination algorithm is proposed based on sparse reconstruction. We transform the problem of estimating ionospheric contamination phase into a sparse optimization problem, then solve it rapidly by the iterative method to get the modulation frequency caused by ionospheric phase contamination. Compared with the existing algorithms, the proposed algorithm in this paper has the following advantages: 1. higher accuracy is obtained under the situation of both fast phase fluctuation and slow phase fluctuation; 2. the proposed algorithm is more robust to noise; 3. real-data processing results of the proposed algorithm are better.