Aiming at developing more biocompatible and economic separation platforms, aqueous biphasic systems (ABS) composed of deep eutectic solvents (DES) and tert-butanol were proposed for the first time. The effects of key factors such as the hydrogen-bond donor (HBD) properties and temperature on the phase-forming ability of DES/tert-butanol ABS were investigated. Meanwhile, syringic acid and eugenol mixtures were selected as model biomolecules to evaluate the efficiency of DES/tert-butanol ABS to use as liquid−liquid extraction systems. The results indicated that DES components migrated preferentially to the bottom phase while tert-butanol was concentrated in the top phase. The more hydrophilic HBD or lower temperature was responsible for greater efficiency to induce the formation of DES/tert-butanol ABS. The reason for phase separation was the incompatibility of the hydrogen-bond acceptor (HBA) and HBD with tert-butanol in aqueous solution, where the higher hydrophilic HBD enriched favorably in the lower phase, allowing for the formation of the DES/tert-butanol ABS. The selective separation of syringic acid and eugenol was a consequence of the HBD characters, temperature, and tie-lines length of the ABS, and they could be greatly separated by using the ABS composed of betaine-xylitol (DES) and tert-butanol at 298.15 K. The highest extraction efficiency of syringic acid and eugenol was 91.64 and 97.62%, respectively. Further, syringic acid and eugenol as well as DES can be recovered and reused by using water as the antisolvent and the vacuum distillation method. This study may be expected to lay a solid foundation for the expansion of DES-based ABS and selective separation of similar biomolecules.