Stably stratified canopy flow in complex terrain has been considered a difficult condition for measuring net ecosystem–atmosphere exchanges of carbon, water vapor, and energy. A long-standing advection error in eddy-flux measurements is caused by stably stratified canopy flow. Such a condition with strong thermal gradient and less turbulent air is also difficult for modeling. To understand the challenging atmospheric condition for eddy-flux measurements, we use the renormalized group (RNG) k–ε turbulence model to investigate the main characteristics of stably stratified canopy flows in complex terrain. In this two-dimensional simulation, we imposed persistent constant heat flux at ground surface and linearly increasing cooling rate in the upper-canopy layer, vertically varying dissipative force from canopy drag elements, buoyancy forcing induced from thermal stratification and the hill terrain. These strong boundary effects keep nonlinearity in the two-dimensional Navier–Stokes equations high enough to generate turbulent behavior. The fundamental characteristics of nighttime canopy flow over complex terrain measured by the small number of available multi-tower advection experiments can be reproduced by this numerical simulation, such as (1) unstable layer in the canopy and super-stable layers associated with flow decoupling in deep canopy and near the top of canopy; (2) sub-canopy drainage flow and drainage flow near the top of canopy in calm night; (3) upward momentum transfer in canopy, downward heat transfer in upper canopy and upward heat transfer in deep canopy; and (4) large buoyancy suppression and weak shear production in strong stability.