Abstract: In order to study the turbulent characteristics of the boundary layer and its effects on the transport of momentum, heat, and water vapor in the Source Region of the Yellow River (SRYR), northeast of the Tibetan Plateau, large eddy simulations are performed for the first time to investigate the fine structure of turbulence in the convective boundary layer (CBL) over two different underlying surfaces (grassland and lake) in the SRYR. GPS soundings and eddy covariance data observed during a field experiment in the Ngoring Lake Basin in summer 2012 are used. It shows that the averaged structures of CBLs over the grassland and lake are in good agreement with the observations, but the characteristics of the turbulent structures over both surfaces show large differences. The budget of turbulent energy, spatial-temporal distribution of turbulent properties, and the structural features of turbulent eddies above the grassland are consistent with the thermal-driven CBL over the land. Organized convective rolls presented at the top of the CBL over the lake. There is larger turbulent intensity at the top of CBL over the lake due to strong entrainment, while the same occurs in the surface layer over the grassland. It is found that the simulated results are sensitive to the horizontal resolution over both surfaces. The denser horizontal resolution applied over the lake helps to improve accuracy in simulation of turbulent kinetic energy and turbulent fluxes of the surface layer and the entrainment layer, and the contributions of various scale’s waves to turbulent fluxes are fully simulated as well. The grid spacings of 100–200 m are recommended to simulate the fine turbulent structure over the grassland if the simulated time is considered.