To test the applicability of the footprint model over complex surface, heat flux data measured from Beijing Xiao Tang Shan heterogeneous field experiment in May 2005 are used. The data from eddy covariance measurements and Large Aperture Scintillometer (LAS) are processed and analyzed by a footprint model, respectively. Because of heterogeneity, the measurement of eddy covariance method seems to be ambiguous, which contains turbulence information from other land covers. The LAS data have a problem of underestimation due to the blending height and ‘source area’ effect. After corrected by the footprint method, they are in good agreement. The results demonstrate that the footprint model is an effective and practical tool to solve the heterogeneous problem in the turbulence flux study.