Iridoid glycosides (IGs) are secondary metabolites found in plants such as the noni plant (Morinda citrifolia L.), known for their diverse biological activities and potential health benefits. Herein, we screened fifteen natural deep eutectic solvents (NADES) and two conventional solvents (CS, 70% (V/V) methanol and 70% (V/V) ethanol) for extraction of IGs from noni fruit pomace. Our findings indicate that non-acidic NADES promote IG extraction. Glycerol/glycine combined with β-cyclodextrin was selected, and a molecular simulation was performed to elucidate the interaction between NADES components and IGs. Further, the structure-activity relationship and interaction mechanisms of IGs with α-glucosidase were investigated using multispectral and molecular docking tools. The results demonstrated that deacetylation of the B-ring's C-10 improved the inhibitory potential of IGs. Deacetylation produces hydrophobic contacts, which enhance the inhibitory effect of deacetylasperulosidic acid on α-glucosides. Additionally, hydrogen bonds and van der Waals forces drive the formation of non-covalent complexes between IGs and enzymes.