Abstract(#br)Forest canopies play a critical role in affecting momentum and scalar transfer. Although there have been recent advances in numerical simulations of turbulent flows and scalar transfer across plant canopies and the atmosphere interface, few models have incorporated all important physical and physiological processes in subcanopy layers. Here we describe and evaluate an advanced multiple‐layer canopy module (MCANOPY), which is developed based largely on the Community Land Model version 4.5 and then coupled with the Weather Research and Forecasting model with large‐eddy simulations (WRF‐LES). The MCANOPY includes a suite of subcanopy processes, including radiation transfer, photosynthesis, canopy layer energy balance, momentum drag, and heat, water vapor, and CO2... exchange between canopy layers and the canopy atmosphere. Numerical schemes for heat and water transport in soil, ground surface energy balance, and soil respiration are also included. Both the stand‐alone MCANOPY and the coupled system (the WRF‐LES‐MCANOPY) are evaluated against data measured in the Canopy Horizontal Array Turbulence Study field experiment. The MCANOPY performs reasonably well in reproducing vertical profiles of mean and turbulent flows as well as second‐order statistical quantities including heat and scalar fluxes within the canopy under unstable stability conditions. The coupled WRF‐LES‐MCANOPY captures major features of canopy edge flows under both neutral and unstable conditions. Limitations of the MCANOPY are discussed for our further work. Our results suggest that our model can be a promising modeling system for a variety of applications to study canopy flows and scalar transport (e.g., CO2).