Despite extensive efforts into the characterization of air pollution during the past decade, real-time characterization of aerosol particle composition above the urban canopy in the megacity Beijing has never been performed to date. Here we conducted the first simultaneous real-time measurements of aerosol composition at two different heights at the same location in urban Beijing from December 19, 2013 to January 2, 2014. The nonrefractory submicron aerosol (NR-PM1) species were measured in situ by a high-resolution aerosol mass spectrometer at near-ground level and an aerosol chemical speciation monitor at 260 m on a 325 m meteorological tower in Beijing. Secondary aerosol showed similar temporal variations between ground level and 260 m, whereas much weaker correlations were found for the primary aerosol. The diurnal evolution of the ratios and correlations of aerosol species between 260 m and the ground level further illustrated a complex interaction between vertical mixing processes and local source emissions on aerosol chemistry in the atmospheric boundary layer. As a result, the aerosol compositions at the two heights were substantially different. Organic aerosol (OA), mainly composed of primary OA (62%), at the ground level showed a higher contribution to NR-PM1 (65%) than at 260 m (54%), whereas a higher concentration and contribution (15%) of nitrate was observed at 260 m, probably due to the favorable gas-particle partitioning under lower temperature conditions. In addition, two different boundary layer structures were observed, each interacting differently with the evolution processes of aerosol chemistry.