The invention discloses a DOA estimation algorithm based on Prony method. The algorithm is suitable for estimating the target azimuth in radar and sonar systems, and is characterized by comprising the following steps that: step 1, the DOA estimation algorithm measurement equation is obtained; step 2, for the uniform linear array, the Prony method is used directly to solve the measurement equation; step 3, for the uniform circular array, the transformation matrix is constructed, and then the measurement equation is solved by Prony method. The technical scheme of the DOA estimation algorithm based on Prony method realizes the target DOA estimation in measuring a platform of the uniform linear array and the uniform circular array, and the estimator performs well under high signal-to-noise ratio condition, no search is required, and the computational complexity is reduced without the feature decomposition. At the same time, the DOA estimation algorithm can break through the Rayleigh limit of the array, and the resolution is higher; moreover, the decoherent operation is not needed under the condition of coherent source, which provides a new method for DOA estimation algorithm.