The potato-rot nematode Ditylenchus destructor (Tylenchida: Anguinidae) causes severe damage to garlic production in Japan. Nematode-contaminated garlic seed cloves are often used for planting, because nematode-infested cloves are difficult to discriminate from healthy ones. To be able to find nematode-infested garlic in a nondestructive way, here this study introduced a novel analytical system of GC–O and GC–MS with heart-cut enrichment technique. The objective of this research was to find an analytical approach to identify the existence of subjectively perceptible odors which derive from the garlic infested with the nematode and to evaluate the effectiveness of those novel analytical systems. Ten odor activities associated with nematode-infested garlic were detected by the system, and “allyl methyl sulfide” and “2-methyl-1-butanol” were identified as major odor compounds (1-propanethiol was candidate). This result suggests that the novel analytical technique introduced in this study delivered sufficient data to identify the odor compounds from infested garlics. Two distinctive odor compounds might be used as indicators to detect nematode-infested garlic cloves with nondestructive way.