Agarwood is resin-containing wood produced by plants that have been injured. It is widely used in herbal medicine, incense, decorative items, and so on. In this study, we conducted resin area statistical analysis, determined starch particle and reducing sugar contents, and performed multivariate statistical analysis of chemical composition by GC–MS and UPLC-Q-TOF-MS to explore the different components in sections cut from an agarwood column, designated as A1–A4. The results showed that after stimulation by Agar-Bit inducer, the internal phloem parenchyma cells of the column started to form agarwood, and then starch granules were converted into soluble reducing sugars and agarwood resin. Section A1 showed rapid loss of starch granules, resulting in higher contents of reducing sugars and resin. The resin areas of agarwood in the respective sections were different, gradually decreasing on going from A1 to A4. Total numbers of metabolites of 87 and 63 were identified by GC–MS and UPLC-Q-TOF-MS, respectively. Of these, 10 and 16 metabolites with significant differences (variable importance projection >1) were selected through multivariate statistical analysis. These metabolites included chromones, sesquiterpenes, alkanes, and fatty acids. Among them, 6-methoxy-2-(2-phenylethyl)chromone and 6,7-dimethoxy-2-(2-phenylethyl)chromone were significant markers detected by both GC–MS and UPLC-Q-TOF-MS, which may be essential substances responsible for differences in the agarwood-forming capacities of the cut sections. In conclusion, there has been limited research on the different agarwood-forming capacities of agarwood columns. Here, we explored the differences in various sections of agarwood through chemical analysis to provide a more comprehensive and in-depth understanding of its constitution.