Low soil temperature stress is a critical factor affecting the root water uptake (RWU) rate of plants. In current land surface models, the RWU amount is determined by the soil water extracted from different soil layers, which calculates by the relative soil water availability and the root fraction of each layer in the rooting zone. The effect of low soil temperature stress is not considered, which may produce biases in the simulation of transpiration. In this study, with the utilization of the in-situ observation data from three FLUXNET sites, we introduced three functions to represent the low soil temperature stress in the Common Land Model (CoLM) and evaluated their effects on the energy fluxes simulation. Then the three low soil temperature stress functions were also evaluated in the global offline simulations by using the FLUXNET-MTE (multi-tree ensemble) data. Results show that the default CoLM overestimates the latent heat flux but underestimates the sensible heat flux in the local spring and early summer at three study sites. By incorporating the low soil temperature stress function into CoLM, the bias in energy flux simulation is significantly reduced. The global offline simulations indicate that considering the effect of low soil temperature stress can improve the model performance on the simulating of the latent heat flux in those high latitude areas. Therefore, we recommend incorporating the effect of low soil temperature stress into land surface models, which is beneficial to increasing the reliability of the models’ results, especially over the cold regions.