Differentiating the chemical compositions of resinite (amber, copal, and resin) is very crucial for determining the botanical origin and chemical compositions of the fossilised amber and copal. This differentiation also assists in understanding the ecological functions of resinite. Headspace solid-phase microextraction-comprehensive two-dimensional (2D) gas chromatography-time-of-flight mass-spectroscopy (HS-SPME-GC × GC-TOFMS) was firstly proposed and utilised in this research to investigate the chemical components (volatile and semi-volatile compositions) and structures of Dominican amber, Mexican amber, and Colombian copal for origin traceability, which were all produced by trees belonging to the genusHymenaea. Principal component analysis (PCA) was used to analyse the relative abundances of each compound. Several informative variables were selected, such as caryophyllene oxide, which was only found in Dominican amber, and copaene, which was only found in Colombian copal. 1H-Indene, 2,3-dihydro-1,1,5,6-tetramethyl- and 1,1,4,5,6-pentamethyl-2,3-dihydro-1H-indene were abundantly present in Mexican amber, which were the critical fingerprints for the origin traceability of amber and copal produced by trees from the genusHymenaeaof various geological places. Meanwhile, some characteristic compounds were closely related to the invasion of fungi and insects; their links with ancient fungi and insect categories were also decoded in this study and these special compounds could be used to further study the plant–insect interactions.