This study proposes a microscale flow model to estimate mean wind speed, fluctuating wind speed and wind direction over complex terrain considering the effects of topography, atmospheric stability, and turbine wakes. Firstly, the effect of topography is considered using Computational Fluid Dynamics (CFD). Next, a mesoscale model is presented to account for the effect of atmospheric stability. The effect of turbine wakes on the mean and fluctuating wind speeds are then represented by an advanced wake model. The model is validated using the measurement data of a wind farm located in the North of Japan. The measured wind data by Lidar at a reference height are horizontally extrapolated to a nearby met mast hub height and validated by a cup anemometer. Moreover, a novel averaging method is proposed to calculate a directional equivalent Monin–Obukhov length scale to account for the effect of atmospheric stability. Finally, the measured wind data at the reference height are vertically extrapolated and validated at the lidar location. The predicted mean and fluctuating wind speeds show good agreement with the measurements.