This is the second part of a study on the assessment of the Noah land surface model (LSM) in simulating surface water and energy budgets in the high-elevation source region of the Yellow River. Here, there is a focus on turbulent heat fluxes and heat transport through the soil column during the monsoon season, whereas the first part of this study deals with the soil water flow. Four augmentations are studied for mitigating the overestimation of turbulent heat flux and underestimation of soil temperature measurements: 1) the muting effect of vegetation on the thermal heat conductivity is removed from the transport of heat from the first to the second soil layer, 2) the exponential decay factor imposed on is calculated using the ratio of the leaf area index (LAI) over the green vegetation fraction (GVF), 3) Zilitinkevich’s empirical coefficient for turbulent heat transport is computed as a function of the momentum roughness length , and 4) the impact of organic matter is considered in the parameterization of the thermal heat properties. Although usage of organic matter for calculating improves the correspondence between the estimates and laboratory measurements of heat conductivities, it is shown to have a relatively small impact on the Noah LSM performance even for large organic matter contents. In contrast, the removal of the muting effect of vegetation on and the parameterization of greatly enhances the soil temperature profile simulations, whereas turbulent heat flux and surface temperature computations mostly benefit from the modified formulation. Further, the nighttime surface temperature overestimation is resolved from a coupled land–atmosphere perspective.