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Sub‐grid topographic heterogeneity has large impacts on surface energy balance and land‐atmosphere interactions. However, the impacts of representing sub‐grid topographic effects in land surface models (LSMs) on surface energy balance and boundary conditions remain unclear. This study analyzed and evaluated the impacts of sub‐grid topographic representations on surface energy balance, turbulent heat flux, and scalar (co‐)variances in the Energy Exascale Earth System Model (E3SM) land model (ELM). Three sub‐grid topographic representations in ELM were compared: (a) the default sub‐grid structure (D), (b) the recently developed sub‐grid topographic structure (T), and (c) high spatial resolution (1KM). Additionally, two different solar radiation schemes in ELM were compared: (a) the default plane‐parallel radiative transfer scheme (PP) and (b) the parameterization scheme (TOP) that accounts for sub‐grid topographic effects on solar radiation. A series of offline simulations with the three grid discretization structures (D, T, and 1KM) and two schemes of solar radiation (TOP and PP) were carried out using the Sierra Nevada, California. 1KM simulations with TOP well capture the spatial heterogeneity of surface fluxes compared to Moderate Resolution Imaging Spectroradiometer remote sensing data. There are significant differences between TOP and PP in the 1‐km simulated surface energy balance, but the differences in mean values and standard deviations become small when aggregated to the grid scale (i.e., 0.5°). The T configuration better mimics the 1KM simulations with TOP than the D configuration and better captures the sub‐grid topographic effects on surface energy balance and boundary conditions. These results underline the importance of representing sub‐grid topographic heterogeneities in LSMs and motivate future research to understand the sub‐grid topographic effects on land‐atmosphere interactions over mountainous areas. Plain Language Summary: Topography has significant impacts on surface energy balance and land‐atmosphere interactions, which has not been well represented in land surface models (LSMs). Our study quantified the impacts of representing sub‐grid topography on surface energy balance and surface boundary conditions in the Energy Exascale Earth System Model (E3SM) land model (ELM). The topounit‐based sub‐grid structure that parsimoniously captures sub‐grid topographic heterogeneity provides a better performance than the default sub‐grid structure in ELM and is computationally efficient. Our study underlines the importance of representing sub‐grid topographic heterogeneities in LSMs and Earth System Models and is promising to promote future research to understand the sub‐grid topographic effects on terrestrial processes and land‐atmosphere interactions over complex terrain. Key Points: The Energy Exascale Earth System Model (E3SM) land model (ELM) component was used to evaluate the impacts of sub‐grid topographic representationsSub‐grid topographic representation has large impacts on surface energy balance and surface boundary conditionsTopounit provides better performance than the default sub‐grid structure in the E3SM land model [ABSTRACT FROM AUTHOR]