Unlike forest, grassland, farmland, and other underlying surfaces, the urban underlying surface is especially complex. Quantification of the urban flux is difficult because of the complex morphological nature of the urban ecosystem. The uneven arrangement of emission sources and sinks also causes measurement to be challenging. Advances in instrumentation, notably the eddy covariance (EC) technique, offer a tool for the direct measurement of representative flux data in urban areas. However, in most urban flux experiments, EC sensors are installed at a certain height, so the measurement results can only reflect the physical processes of a specific point or part of the underlying surface, and spatial representation has become a problem that cannot be ignored. Scalar flux footprint estimation was created to solve this problem. In this study, we used seven levels of EC data from the Beijing 325 m meteorology tower. The source areas and footprint were examined at different heights and in different wind directions under stable, neutral, and unstable conditions. We found that under stable conditions, the source area has a strong relationship with the upwind direction, but there is no such relationship under unstable conditions. The source area is much larger under stable conditions than under unstable conditions for the same height. Measurement data at 8 and 16 m cannot represent the flux of the urban underlying surface, but data from 47 m and higher can represent this flux, and data from 280 m represent the suburban and urban average. For conditions of the same stability, the source area becomes larger as the height increases. In addition, we obtained a linear relationship between measurement height and source area. This linear relationship is useful for evaluating the flux source area of other heights.