Matrix Pencil method is one of the promising method to estimate DOA in non-stationary, multi-path coherent environment. Not only the Matrix Pencil Method offers better resolution than the conventional approach using covariance matrix, but also it is computationally very efficient. In this paper, we presented an effect of unbalanced data weighting in the formulation of the Matrix Pencil method. A new formulation has been suggested to mitigate the effect of unbalanced data weighting. Numerical simulation demonstrated that the proposed method can successfully eliminate the problem of unbalanced data weighting.