Chuju, a cultivar of Chrysanthemum morifolium, has been traditionally cultivated for over 2000 years in China for both ornamental and medicinal purposes. To date, investigations into the chemical composition of this plant have indicated that it contains compounds with extensive biological activities, although detailed information on the chemical composition of Chuju remains scarce. In the present study, the chemical compositions of Chuju flowers were investigated across five sites in the core Chuju planting area in Anhui province, China. Analytical pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS) was used to explore variations in flower chemical fingerprints from different Chuju planting sites. The study identified approximately 200 components in Chuju flowers and stems, including high levels of fatty acids, lipids, polysaccharides and terpenoids. Multivariate statistical analysis indicated that 16 chemical compounds were influential determinants of the chemical fingerprint and could be used to distinguish two clusters in the five core planting areas. The established Py-GC/MS analytical workflow could provide a basis for determining the chemical fingerprints of Chuju and help elucidate that products contain a reproducible content of bioactive compounds and overall quality for potential development of health and medicinal purposes.