The effects of the scale/intensity of free-stream turbulence on the statistical and structural characteristics of boundary layer turbulence were focused on. Four types of turbulent boundary layer with free-stream turbulence of different scales and intensities were generated by large eddy simulation with proportional-integral-differential control and linear forcing. The statistical properties and spatial structure of flow and passive scalar fields, which were separated into large- and small-scale components using a spatial filter, were evaluated. The results suggested that large-scale structures in free-stream turbulence penetrate into the boundary layer, resulting in increased turbulent energy, scalar variance, Reynolds stress, and turbulent scalar flux and strengthened coherent large-scale motions in the boundary layer. Moreover, the large-scale motions in the free stream also modulated the amplitude of small-scale turbulence near the wall. The small-scale motions in the free stream, on the other hand, had a negligible effect.