Background: Agarwood is a resinous heartwood produced in certain Aquilaria species that is often used as a spice and Chinese medicine materials. Objectives: This study aimed to comprehensively evaluate the agarwood quality of different species under the same inducer as well as different inducers of the same species. Materials and Methods: The GC-MS data of agarwood were retrieved by AMDIS to obtain 47 secondary metabolites. Combined with multivariate statistical analysis, 12 secondary metabolites were identified as potentially representing the differences between A. malaccensis and A. sinensis. The gray correlation degree and TOPSIS method were used to comprehensively grade 18 characters, including the AEC, the content of agarotetrol, the apparent abundance of GC-MS fingerprint, and the 15 secondary metabolites representing the 58 batches of samples. The OD values representing the overall desirability of ri (gray correlation degree) and ci (TOPSIS) were ranked, with a higher ranking reflecting, better agarwood quality. Results: The ranking results demonstrated that the agarwood samples of the top 33 in OD value were all induced by FAM71, whereas the agarwood samples of the top 23 were all from A. malaccensis. The agarwood of A. sinensis induced by FA had the lowest OD value. Conclusion: The study demonstrated that the quality of agarwood from A. malaccensis was better than that of A. sinensis using the same inducer of FAM71. In the same species of A. sinensis, the quality of agarwood produced by FAM71 was better than that induced by formic acid alone or NA8 alone. This study provided a theoretical basis for the selection of high-quality agarwood inducer and tree species, as well as a reference basis for the efficient production of agarwood in the actual production process.