The main non-biodegradable compounds (soluble microbial product – SMP) of wastewater from the Maotai aromatic factories, located in the Chishui river region, were analyzed by UV spectroscopy, and by solid-phase extraction followed by gas chromatography coupled to mass spectrometry, after a two-stage biochemical treatment. The UV-Vis spectra revealed that the wastewater contained two double-bonds in conjugated systems (conjugated diene or α, β- unsaturated ketone, etc.) and simple non-conjugated chromophores containing n electrons from carbonyl groups or the like. The residual organic non-biodegradable substances were identified using SPE-GC/MS analysis as complex polymers containing hydroxyl, carbonyl, and carboxyl functional groups with multiple connections to either benzene rings or heterocyclic rings. As these compounds are difficult to remove by conventional biochemical treatments, our findings provide a scientific basis for the design of efficient new strategies to remove SMP from wastewater.