Morphological analysis has been frequently applied in archaeobotany. Recently, increasing studies have been conducted on the identification of biomarkers in archaeobotanical materials, which are rarely attached to morphological analysis. To improve the interpretability of biomarker analysis, the localisation of characteristic biomarkers in ancient samples is needed. We analysed characteristic lignans in ancient/modern sesame seeds via matrix-assisted laser desorption ionisation quadrupole time-of-flight mass spectrometry imaging (MSI), testifying the potential of MSI in a detailed discussion of ancient plant use practices. The MSI distributions of sesamin and sesamolin shared similar traits in modern and ancient sesame seeds while their MSI signals were inhibited by lipidic substances in in situ MSI tests. Besides targeted biomarker characterisation, nontargeted MSI analysis showed potential to reveal plant material treatment process. Botanical biomarker distribution traits were studied for the first time in archaeobotany. The MSI created a visualised colour plot with localised compound distributions, in which archaeologists can visually aid their study of plant use in antiquity. This, in some cases, provides key information for understanding the livelihoods of ancient people.