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This study develops an unstructured mesh generation tool for land surface modeling using a multi‐scale hexagon discrete mesh. The tool can automatically determine the required mesh resolution for different regions based on multi‐objective criteria such as elevation, slope, land cover, and land use. The refined unstructured meshes demonstrate significant enhancement in the representation of spatial heterogeneity. The tool is coupled with the Common Land Model (CoLM) to enable land surface simulations using unstructured meshes. Evaluations focused on runoff, river discharge, and inundation indicate improved model performance compared to traditional structured mesh‐based CoLM simulations under the same computational cost constraints. This tool provides new capabilities for more efficiently capturing localized land surface processes and extreme events. Plain Language Summary: The traditional square mesh cells used in land surface models (LSMs) have limitations in capturing the hydrological processes in regions with spatial solid heterogeneity, for example, mountains and forest‐grass transition zones. This study develops a new tool to generate unstructured mesh with flexible cell shapes and sizes. The tool can automatically adjust the mesh resolution based on the various land surface features. Thus, it can represent better spatial differences in elevation, vegetation, soil, etc. For example, it can use finer meshes for mountains and coarser meshes for desert areas. The new unstructured meshes are coupled with an existing LSM called Common Land Model. Model testing shows improved runoff, river discharge, and flooding simulation compared to traditional square mesh models under the same computation cost. Overall, the new unstructured mesh modeling approach enables more efficient and accurate simulation of localized land processes and extreme events, for example, droughts and floods. It has significance for disaster prevention and environmental studies. Key Points: An unstructured mesh generation tool for land surface models can automatically refine resolution based on multi‐objective landscape criteriaCoupling refined unstructured meshes with the Common Land Model (CoLM) model improves local hydrological simulation compared to traditional mesh‐based CoLMThe tool enables more efficient and accurate modeling of localized land surface processes and extreme events such as droughts and floods [ABSTRACT FROM AUTHOR]