Estimation of covariance matrix and its inverse is of great importance in multivariate statistics with broad applications such as dimension reduction, portfolio optimization, linear discriminant analysis and gene expression analysis. However, accurate estimation of covariance or inverse covariance matrices is challenging due to the positive definiteness constraint and large number of parameters, especially in the high-dimensional cases. In this thesis, I develop several approaches for estimating large covariance and inverse covariance matrices with different applications. In Chapter 2, I consider an estimation of time-varying covariance matrices in the analysis of multivariate financial data. An order-invariant Cholesky-log-GARCH model is developed for estimating the time-varying covariance matrices based on the modified Cholesky decomposition. This decomposition provides a statistically interpretable parametrization of the covariance matrix. The key idea of the proposed model is to consider an ensemble estimation of covariance matrix based on the multiple permutations of variables. Chapter 3 investigates the sparse estimation of inverse covariance matrix for the highdimensional data. This problem has attracted wide attention, since zero entries in the inverse covariance matrix imply the conditional independence among variables. I propose an orderinvariant sparse estimator based on the modified Cholesky decomposition. The proposed estimator is obtained by assembling a set of estimates from the multiple permutations of variables. Hard thresholding is imposed on the ensemble Cholesky factor to encourage the sparsity in the estimated inverse covariance matrix. The proposed method is able to catch the correct sparse structure of the inverse covariance matrix. Chapter 4 focuses on the sparse estimation of large covariance matrix. Traditional estimation approach is known to perform poorly in the high dimensions. I propose a positive-definite estimator for the covariance matrix using the modified Cholesky decomposition. Such a decomposition provides a exibility to obtain a set of covariance matrix estimates. The proposed method considers an ensemble estimator as the center" of these available estimates with respect to Frobenius norm. The proposed estimator is not only guaranteed to be positive definite, but also able to catch the underlying sparse structure of the true matrix. / Ph. D.