Vertical profiles of isoprene and monoterpenes were measured by a proton transfer reaction-time of flight-mass spectrometry (PTR-ToF-MS) at heights of 3, 15, 32, 64, and 102 m above the ground on the Institute of Atmospheric Physics (IAP) tower in central Beijing during the winter of 2016 and the summer of 2017. Isoprene mixing ratios were larger in summer due to much stronger local emissions whereas monoterpenes were lower in summer due largely to their consumption by much higher levels of ozone. Isoprene mixing ratios were the highest at the 32 m in summer (1.64 ± 0.66 ppbV) and at 15 m in winter (1.41 ± 0.64 ppbV) with decreasing concentrations to the ground and to the 102 m, indicating emission from the tree canopy of the surrounding parks. Monoterpene mixing ratios were the highest at the 3 m height in both the winter (0.71 ± 0.42 ppbV) and summer (0.16 ± 0.10 ppbV) with a gradual decreasing trend to 102 m, indicting an emission from near the ground level. The lowest isoprene and monoterpene mixing ratios all occurred at 102 m, which were 0.71 ± 0.42 ppbV (winter) and 1.35 ± 0.51 ppbV (summer) for isoprene, and 0.42 ± 0.22 ppbV (winter) and 0.07 ± 0.06 ppbV (summer) for monoterpenes. Isoprene in the summer and monoterpenes in the winter, as observed at the five heights, showed significant mutual correlations. In the winter monoterpenes were positively correlated with combustion tracers CO and acetonitrile at 3 m, suggesting possible anthropogenic sources.