Abstract: Kernel function method has been successfully used for the estimation of a variety of function. By using the kernel function theory, an imputation method based on Epanechnikov kernel and its modification were proposed to solve the problem that missing data in compositional caused the failures of existing statistical methods and the k-nearest imputation didn't consider the different contributions of the k nearest samples when it used them to estimated the missing data. The experimental results illustrate that the modified imputation method based on Epanechnikov kernel get a more accurate estimation than k-nearest imputation for compositional data.