Large-scale coherent structures are systematically investigated in terms of their geometric attributes, importance toward describing turbulent exchange of energy, momentum and mass as well as their relationship to landscape features in the context of land-atmosphere interaction. In the first chapter, we present the motivation of this work as well as a background review of large-scale coherent structures in land-atmosphere interaction. In the second chapter, the methodology of large-eddy simulation (LES) and the proper orthogonal decomposition (POD) is introduced. LES was used to serve as a virtual laboratory to simulate typical scenarios in land-atmosphere interaction and the POD was used as the major technique to educe the coherent structures from turbulent flows in land-atmosphere interaction. In the third chapter, we justify the use of the LES to simulate the realistic coherent structures in the atmospheric boundary layer (ABL) by comparing results obtained from LES of the ABL and direct numerical simulation (DNS) of channel flow. In the fourth chapter, we investigate the effects of a wide range of vegetation density on the coherent structures within the air space within and just above the canopy (the so-called canopy sublayer, CSL). The fifth chapter presents an analysis of the coherent structures across a periodic forest-clearing-forest transition in the steamwise direction. The sixth chapter focuses on the role of coherent structures in explaining scalar dissimilarity in the CSL. The seventh chapter summarizes this dissertation and provides suggestions for future study.