Aqueous two-phase systems (ATPS) are considered a new type of green separation system, but their low selectivity to target molecules limits their practical application. In this study, we used surfactant@MWCNT as an adjuvant to improve the selectivity of PEG/(NH4)2SO4 ATPS. The surfactants used include Triton X-100 (TX-100), Tween 80, sodium dodecyl sulfate (SDS), sodium dodecyl benzenesulfonate (SDBS), and bis(2-ethylhexyl)sulfosuccinate sodium salt (AOT). Nine aromatic compounds, including syringic acid, vanillin, tryptophan, phenylalanine, tyrosine, mandelic acid, theophylline, theobromine, and cephalexin, were selected as model extracts. The results showed that the use of the surfactant@MWCNT composite as an adjuvant significantly improved the selectivity of the ATPS toward syringic acid among the nine extracts. Moreover, the selectivity of the ATPS for syringic acid with the TX-100/MWCNT composite as the adjuvant is better than that with the Tween 80/MWCNT composite as the adjuvant, followed by that with the anionic surfactant/MWCNT composite as the adjuvant. The enhanced selectivity of ATPS by the surfactant/MWCNT composite is ascribed to the spatial effect and the electrostatic and hydrophobic interactions between the extract and the surfactant adsorbed on the MWCNT.