Structure elucidation of volatile aromatic isomers at trace level has long been considered as an elusive task, due to their structural similarities and similar polarities, even with the aid of many spectroscopic techniques such as mass spectrometry and nuclear magnetic resonance (NMR) spectroscopy. Single-crystal X-ray diffraction (SCD) is recognized as one of the most powerful structural elucidation techniques. The recently developed crystalline sponge method overcomes the intrinsic limitation of SCD that the target molecules must be single crystals, being able to analyze non-crystalline and trace-amount compounds without any special treatment. In order to investigate whether the crystalline sponge method could be used for the structure elucidation of closely related isomers or other volatile and even oily compounds in complex mixtures at trace level, we combined HPLC separation with the crystalline sponge method for X-ray crystallographic analysis. In this paper, two pairs of volatile aromatic isomers including cis/trans isomers of asarone and positional isomers of carvacrol and thymol, as well as the main volatile component in essential oil extracted from Acorus Tatarinowii, were first isolated by HPLC and encapsulated into the crystalline sponge then elucidated by X-ray crystallographic analysis. Direct observation of these volatile compounds by X-ray crystallography was achieved using only microgram quantities without crystallization or derivatization. Unambiguous identification of these compounds was realized without reference standards. This strategy offers a promising platform capable of providing high-confidence detailed structural information of closely related isomers as well as other volatile and even oily compounds in complex mixtures in microgram quantities.