The widely accepted method for detecting trace odor compounds such as 2-methylisoborneol (2-MIB) requires high-cost solid-phase microextraction coupled with gas chromatography-tandem mass spectrometry (SPME-GC/MS). As for now, cases that directly used SPME-GC/MS in the field are unseen, and most detection activities are still carried out in rigorous laboratory conditions. However, lengthy logistics and storage issues can compromise sample conditions, underscoring the significance of on-site detection methods. Here, we reported molecularly imprinted polymers-enabled headspace extracting and electrochemical sensing (MHEES) with the core feature of using the same piece of MIP for both headspace extracting and electrochemical sensing, allowing rapid on-site detection of trace 2-MIB in natural water bodies with a total cost of less than $2.10 per test. MHEES demonstrated exceptional sensitivity during extensively repeated laboratory experiments, achieving a detection limit of 3.7 ng∙L−1 and a standard deviation of 4.58 %. The practicality of MHEES was confirmed by conducting two rounds of on-site analyses on different reservoirs with fluctuating seasonal concentrations of 2-MIB. The developing flow of MHEES, from molecules docking to on-site application, was rigorous and could be cross-referenced to related research. The proposed MHEES design can potentially revolutionize the field of analytical chemistry by providing a versatile and affordable platform for on-site volatile compounds detection. It can readily adapt to various organic compounds and effectively address real-world challenges such as monitoring emerging pollutants, tracing disease biomarkers in body fluids, inspecting food safety, identifying chemical reaction intermediates, and supporting healthcare applications.