Turbulence statistics such as flux-variance relationship are critical information in measuring and modeling ecosystem exchanges of carbon, water, energy, and momentum at the biosphere-atmosphere interface. Using a recently proposed mathematical technique, the Hilbert-Huang transform (HHT), this study highlights its possibility to quantify impacts of non-turbulent flows on turbulence statistics in the stable surface layer. The HHT is suitable for the analysis of non-stationary and intermittent data and thus very useful for better understanding the interplay of the surface layer similarity with complex nocturnal environment. Our analysis showed that the HHT can successfully sift non-turbulent components and be used as a tool to estimate the relationships between turbulence statistics and atmospheric stability in complex environments such as nocturnal stable boundary layer.