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Based on observation data from urban observation stations in Nanjing and Suzhou at two heights in the roughness sublayer above the canopy and observation data at three heights in the SORPES station at the Xianlin Campus of Nanjing University in a suburban area, the representativeness of land-atmosphere turbulent flux exchange and the energy balance over complex underlying surfaces were analyzed. The results indicated that in the roughness sublayer above the canopy, the nearsurface momentum flux, sensible heat flux, and latent heat flux increase with height, and the observation value of the surface albedo increases with height. However, the observation value of the net radiation decreases with height, thus resulting in a change in the urban surface energy budget with height. At the SORPES station in the Xianlin Campus of Nanjing University located in a hilly area, the momentum flux, sensible heat flux, and latent heat flux of the ground observation field significantly differed from those of the two heights on the tower, while the two heights on the tower were extremely close. These results indicate that the flux observation over the complex underlying surface exhibits adequate local representativeness only when it is conducted at a higher altitude above the ground. The turbulent flux observation results at a lower altitude in urban areas are underestimated, while the turbulent flux observation results near the surface produce a large deviation over the underlying hilly complex.