Abstract Bronsted acidic ionic liquid was introduced in microwave assisted extraction procedure to simultaneously extract pectin and naringin from the albedo part of pomelo peels. The process for the extraction of pectin and naringin was optimized by a dual response surface methodology. The optimal conditions as follows: [HO 3 S(CH 2 ) 4 mim]HSO 4 concentration of 10 mmol/L, microwave irradiation time of 15 min, liquid–solid ratio of 26 mL/g, and microwave irradiation power of 331 W. Under the optimum conditions, the yields reached to 291.60 ± 7.25 mg/g for pectin and 8.38 ± 0.20 mg/g for naringin. [HO 3 S(CH 2 ) 4 mim]HSO 4 enjoyed excellent solvent effect for the extraction of pectin and naringin in microwave assisted extraction method in comparing with reference solvents. Fourier transform infrared spectroscopy, scanning electron microscope, and atomic force microscope were employed for the characterization analysis of pectin. Interestingly, the pectin extracted with [HO 3 S(CH 2 ) 4 mim]HSO 4 aqueous solution possessed relatively low degree of esterification and rough, hard and network structures which were apparently different with that extracted with hydrochloric acid solution. Additionally, 190.37 ± 3.28 mg naringin with a purity of 95.23% ± 1.3% were gained from 50 g albedo part of pomelo peels and confirmed by nuclear magnetic resonance, Fourier transform infrared spectroscopy, and mass spectroscopy analysis. This study provides a promising paradigm in modern separation science for the extraction of natural products from plant sources.