A number of studies have reported that the traditional eddy covariance (EC) method generally underestimated vertical turbulent fluxes, leading to an outstanding non-closure problem of the surface energy balance (SEB). Although it is recognized that the enlarged surface energy imbalance frequently coincides with the increasing wind shear, the role of large eddies in affecting the SEB remains unclear. On analyzing data collected by an EC array, considerable horizontal inhomogeneity of kinematic heat flux is observed. The results show that the combined EC method that incorporates the spatial flux contribution increases the kinematic heat flux by 21% relative to the traditional EC method, improving the SEB closure. Additionally, spectral analysis indicates that large eddies with scales ranging from 0.0005 to 0.01 (in the normalized frequency) mainly account for the horizontal inhomogeneity of kinematic heat flux. Under unstable conditions, this process is operating upon large eddies characterized by enlarged asymmetric turbulent flux transport. With enhanced wind shear, the increment of flux contribution associated with sweeps and ejections becomes disproportionate, contributing to the horizontal inhomogeneity of kinematic heat flux, and thus may explain the increased SEB non-closure