In this paper, a new method is presented for heart sound signal processing in statistical domain. The multiple components obtained from the conventional linear transformation are possibly irrelevant, but usually do not possess the characteristics of statistical independence. First, the definition and obtaining method of independent function element are discussed; the method of signal decomposition and reconstruction based on the independent function element, not only inherits the advantages of linear transformation, but also has the capability of signal representation in the statistical domain. After that, the application of independent function element in heart sound signal analysis is analyzed in detail. The validity and practicability of the method are demonstrated through two experiments.