Volatile organic compounds (VOCs) are important pollutants that affect air quality and atmosphere-ecosystem interactions. Atmospheric sampling onboard a multicopter unmanned aerial vehicle (UAV), serving as an economical and flexible measurement technique, collects valuable VOC data sets at intermediate spatial scales of hundreds of meters. In this study, we deployed a UAV-based VOC sampler in South China and conducted VOC samplings at two locations over the canopy of a subtropical forest. The collected VOC samples were analyzed offline by gas chromatography-mass spectrometry. Isoprene and α-pinene, two dominant biogenic VOCs, showed day-to-night variations that were consistent with their emission patterns. High concentrations of ozone and aromatic VOCs indicate a strong influence of anthropogenic pollution in this forest area. Meanwhile, high ratios of the concentrations of methacrolein and methyl vinyl ketone to isoprene were observed, which are consistent with the possibly fast atmospheric oxidation under the anthropogenic influence. Significant daytime concentration differences were observed between the two sampling locations for isoprene. The analysis by a gradient transport model suggests a large isoprene emission heterogeneity along the mountain slope at the scale of hundreds of meters for subtropical forests, which has not yet been well represented in most biosphere emission models. Strong eddy diffusion caused by the valley breeze may also contribute to the observed concentration differences.