The detection of harmonic and the traditional Prony algorithm is sensitive to noise .In order to calculate the characteristic parameters of harmonics and inter-harmonics accurately, a harmonic parameter estimation method based on mathematical morphology and improved Prony algorithm is proposed. The main idea of this method is to construct morphological filter with mathematical morphology to denoise. The shortcomings of the traditional Prony algorithm for noise sensitivity can be overcome. Then the harmonic signal after noise removal is underway by improved Prony. Through MATLAB programming analysis of harmonic signal, it is found that this method can get high-accuracy amplitude, frequency and phase parameters under noises. The feasibility and effectiveness of the method are verified .