The datasets presented in this article consist of detailed chemical analyses of three different species of Aquilaria using GC-MS and GC-FID techniques. The datasets consist of two samples from each of the three species of Aquilaria, specifically A. crassna (designated as ACS1 and ACS2), A. malaccensis (designated as AMS1 and AMS2), and A. subintegra (designated as ASS1 and ASS2). The datasets include information on the retention times, Tr (min), peak area (%), identified compounds, molecular formulas, molecular weights, identification modes, and similar chemical compounds found in every species of Aquilaria. in each sample, were meticulously tabulated in MS Excel. Concurrently, the chemical analyses collectively unveil that agarwood oil is predominantly composed of a mixture of compounds. These compounds can be categorized into four distinct groups: carboxylic acid, other compounds, sesquiterpene, and sesquiterpenoid. This comprehensive dataset facilitates a thorough understanding of the chemical profiles and analytical nuances across the different Aquilaria species, enhancing the robustness and interpretability of the datasets.