Radix Paeoniae Alba, the dried root of Paeonia lactiflora Pall., contains characteristic monoterpene glycosides, but efficient recovery of these polar constituents remains challenging. This study developed an ionic liquid-assisted sequential ultrasound–microwave extraction method and evaluated paeoniflorin, oxypaeoniflorin and albiflorin by HPLC as multi-marker responses. Among the ionic liquids tested, 1-propyl-3-methylimidazolium dihydrogen phosphate showed the best extraction response. Box–Behnken response surface optimization gave practical extraction conditions of a solid-to-liquid ratio of 1:26 g/mL, ionic liquid concentration of 0.12 mol/L and ultrasound time of 22 min. Under these conditions, paeoniflorin and total marker glycosides reached 29.12 and 34.98 mg/g dry material, respectively, representing increases of 32.4% and 34.5% compared with conventional reflux extraction. UPLC-QTOF-MS profiling provided complementary chemical profile information for the optimized extract and tentatively annotated Paeonia-related monoterpene glycoside derivatives, galloylated glucose derivatives and polyphenolic constituents. Electrostatic potential, SAPT and non-covalent interaction analyses, supported by ¹H NMR chemical shift perturbation, suggested possible hydrogen bonding, electrostatic and dispersion interactions between paeoniflorin and the selected ionic liquid. These results support the optimized process as an efficient extraction approach and provide molecular interaction insights into ionic liquid-assisted recovery of monoterpene glycosides.