The objective of this study is to improve the computational efficiency of the enhanced automated multilevel substructuring (EAMLS) method (Kim et al., 2015) for dealing with large finite element models in structural dynamics. In the EAMLS method, the compensation procedure of the residual mode effect is a bottleneck resulting in a large computational cost. The original EAMLS method indeed cannot be used for finite element models with more than one million degrees of freedom in personal computers. An improvement in the computational efficiency is achieved by an interface subspace reduction and a new compensation procedure derived by residual flexibility matrices for only bottom-level substructures. Through this approach with submatrix level computations, the computation time and memory requirements are significantly reduced. Several numerical examples are presented to show the effectiveness of the proposed method.