Quantifying the microclimate of a tall and complex tropical forest is quite challenging because of the difficulty in accessing the canopy. Traditional ground-referenced methods may underestimate the contribution of canopy heterogeneity to structuring the vertical profiles of forest microclimate. The present study examined how the reference height affects vertical variation of microclimate in a tropical rainforest in southwest China, based on both ground- and canopy-referenced approaches. The results show that the canopyreferenced approach yielded a higher model fit than did the ground-referenced method, and only canopy-referenced method could detect two thresholds in the leaf area index at approximately -22.6 +/- 2.7 m and -36.6 +/- 6.6 m below the canopy top; the higher threshold is consistent with thresholds of the annual mean temperature, the diurnal ranges of air temperature, and the relative humidity in the vertical profile; while the lower threshold is similar with the breakpoints of annual mean relative humidity, the annual ranges of air temperature and the relative humidity along the profile. The discontinuous variance in the microclimatic factors was due to the canopy structure in the vertical profile. Selecting the top of the canopy as the reference height could be a better approach for quantifying the microclimatic profiles in the studied forest, and this approach can improve our understanding of the effects of the vertical stratification of microclimates on species composition and diversity in this forest.