To evaluate the performance of hydrophobic deep eutectic solvents (HDESs) and explore their capacity to extract flavonoids from rapeseed pollen, menthol and betaine were selected as hydrogen bond acceptors to prepare a series of HDESs. The structure and physicochemical properties of these HDESs were comprehensively characterized using infrared spectroscopy, rotational rheometry, and differential scanning calorimetry. The study found that the synthesized HDESs exhibited a blue shift in their characteristic infrared absorption peaks compared to the original components. Rheological analysis indicated that their viscosity remained largely unaffected by shear rate, with the menthol-lauric acid system demonstrating relatively low viscosity. Thermal property analysis revealed a significant decrease in the melting point of the synthesized HDESs. HDESs synthesized from menthol-lauric acid exhibited the best extraction efficiency for rapeseed pollen flavonoids. Through single-factor experiments and response surface methodology, the optimal extraction conditions were temperature 61℃, extraction time 85min, and solid-liquid ratio of 1∶25g/mL. Under these conditions, the extraction rate of flavonoids reached 7.209%, which was close to the predicted value, confirming the reliability and practical application potential of the optimized model. Through UPLC-Q-Orbitrap MS component analysis, 33 compounds were identified in the rapeseed pollen flavonoid extract. Among them, naringin chalcone showed the highest content at 295.3157ng/mg, followed by other relatively high-content compounds including kaempferol-3-O-glucoside (64.0583ng/mg), naringenin (56.8966ng/mg), quercetin-3-O-glucoside (18.6507ng/mg), benzoic acid (15.9760ng/mg), p-coumaric acid (10.7606ng/mg), and kaempferol (8.8864ng/mg). The results of this study indicated that the use of HDESs as a novel and efficient extraction approach demonstrated significant advantages for the extraction of rapeseed pollen flavonoids.